Kits for detecting hev nucleic acid

ABSTRACT

Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of Hepatitis E Virus (HEV) nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/012,946, filed Sep. 4, 2020, which is a continuation of U.S. patentapplication Ser. No. 16/015,539, filed Jun. 22, 2018, now issued as U.S.Pat. No. 10,815,541, which is a division of U.S. patent application Ser.No. 14/460,180, filed Aug. 14, 2014, now issued as U.S. Pat. No.10,047,406, which claims the benefit under 35 U.S.C. § 119(e) of U.S.Provisional Application No. 61/865,848, filed Aug. 14, 2013, and of U.S.Provisional Application No. 61/941,303, filed Feb. 18, 2014. Each of theforegoing applications is incorporated herein by reference in itsentirety.

REFERENCE TO SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII Copy, created on Jun. 15, 2021, isnamed “GP292-03UT1_Seq_List_ST25” and is 26,646 bytes in size.

BACKGROUND OF THE INVENTION

Hepatitis E Virus (HEV) is a single-stranded, positive-sense RNA virusclassified in the family Hepeviridae and the sole member of the genusHepevirus, of which mammalian HEV and avian HEV are the two major knownspecies. Dalton et al., Lancet Infect. Dis. 8:698-709, 2008; Baylis etal., J. Clin. Microbiol. 49:1234-1239, 2011. Mammalian HEV, having areservoir in pigs and potentially other mammals, is a major cause ofacute hepatitis in humans. See Dalton et al., supra. The virus istransmitted primarily via the fecal-oral route and is associated withsporadic infections and epidemics in developing countries, particularlyin areas with poor sanitation and weak public health infrastructures. Indeveloped countries, HEV infection has been considered rare, occurringprimarily in individuals infected while traveling to regions where thevirus is endemic. Recently, however, autochthonous infections are beingreported more frequently in developed regions, including North America,Europe, Japan, New Zealand, and Australia. Autochthonous hepatitis E indeveloped countries is, therefore, more common than previouslyrecognized, and may be more common than hepatitis A. Dalton et al.,Lancet Infect. Dis. 8:698-709, 2008.

Four major genotypes of HEV are known to cause infections in humans.Baylis et al., supra. Clinical features of HEV infection can includemild to severe hepatitis as well as subacute liver failure. See, e.g.,Pina et al., J. Hepatol. 33:826-833, 2000; Sainokami et al., J.Gastroenterol. 39:640-648, 2004; Tsang et al., Clin. Infect. Dis.30:618-619, 2000; Widdowson et al., Clin. Infect. Dis. 36:29-33, 2003;Dalton et al., Eur. J. Gastroenterol. Hepatol. 20:784-790, 2008. HEVinfection has a poor prognosis in pregnant women, as well as individualshaving pre-existing chronic liver disease. See Borkakoti et al., J. Med.Virol. 85:620-626, 2013; Baylis et al., supra. Diagnostic testing forHEV in patients with hepatitis symptoms is important, particularly forpatients in which other causes of acute hepatitis have been excluded.See Baylis et al., supra; Waar et al., J. Clin. Virol. 33:145-149, 2005.

Accordingly, there is a need for compositions, kits, and methods fordetecting the presence or absence of HEV in a specimen with highspecificity and sensitivity. Such compositions, kits, and methods wouldbe particularly useful for the diagnosis of HEV, for the screeningand/or monitoring of the presence of HEV in a blood or plasma donation,or for monitoring a patient's response to treatment. The presentinvention meets these and other needs.

SUMMARY OF THE INVENTION

In one aspect, the present invention provides a combination of at leasttwo oligomers for determining the presence or absence of hepatitis Evirus (HEV) in a sample. The oligomer combination includes at least twoamplification oligomers for amplifying complementary nucleic acidstrands of a target region of an HEV target nucleic acid, where

-   -   (a) at least one amplification oligomer is selected from (i) an        oligomer comprising a target-hybridizing sequence that is from        about 14 to about 23 contiguous nucleotides contained in the        sequence of SEQ ID NO:63 and that includes at least the sequence        of SEQ ID NO:26, including RNA equivalents and DNA/RNA chimerics        thereof, and (ii) an oligomer comprising a target-hybridizing        sequence that is from about 14 to about 23 contiguous        nucleotides contained in the sequence of SEQ ID NO:16, including        RNA equivalents and DNA/RNA chimerics thereof; and    -   (b) at least one amplification oligomer comprises a        target-hybridizing sequence that is from about 17 to about 28        contiguous nucleotides contained in the sequence of SEQ ID NO:47        and that includes at least the sequence of SEQ ID NO:25,        including RNA equivalents and DNA/RNA chimerics thereof.

Suitable amplification oligomers as specified above in (a) includeoligomers comprising a target-hybridizing sequence selected from SEQ IDNO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ IDNO:34, SEQ ID NO:35, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ IDNO:61, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66,including RNA equivalents and DNA/RNA chimerics thereof. In somepreferred variations, an amplification oligomer of (a) comprises atarget-hybridizing sequence selected from SEQ ID NO:29, SEQ ID NO:31,SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:61,SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66, includingRNA equivalents and DNA/RNA chimerics thereof. In some embodiments, anamplification oligomer of (a) comprises a target-hybridizing sequencethat is from about 14 to about 20 nucleotides contained in the sequenceof SEQ ID NO:13 (e.g., SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:65, or SEQ ID NO:66).

In certain variations, an amplification oligomer as specified in (a)comprises a target-hybridizing sequence that is from 15 to 17nucleotides contained in the sequence of SEQ ID NO:16 and that includesat least the sequence of SEQ ID NO:27, including RNA equivalents andDNA/RNA chimerics thereof (e.g., a target-hybridizing sequence selectedfrom SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, and SEQ ID NO:32,including RNA equivalents and DNA/RNA chimerics thereof). In someembodiments, an amplification oligomer of (a) comprises atarget-hybridizing sequence of SEQ ID NO:28, including RNA equivalentsand DNA/RNA chimerics thereof (e.g., a target-hybridizing sequenceselected from SEQ ID NO:29 and SEQ ID NO:32, including RNA equivalentsand DNA/RNA chimerics thereof).

Suitable amplification oligomers as specified above in (b) includeoligomers comprising a target-hybridizing sequence selected from SEQ IDNO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:45, SEQ IDNO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, and SEQID NO:56, including RNA equivalents and DNA/RNA chimerics thereof. Insome preferred variations, an amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:24 and SEQ ID NO:56,including RNA equivalents and DNA/RNA chimerics thereof. In otherpreferred variations, an amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:22, SEQ ID NO:23,SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:51, including RNA equivalentsand DNA/RNA chimerics thereof. In certain variations comprising anamplification oligomer having the target-hybridizing sequence of SEQ IDNO:56, the nucleobase at position 1 of SEQ ID NO:56 is guanine (G)(i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA chimeric thereof).

In some embodiments, a combination of at least two oligomers as aboveincludes an amplification oligomer as specified in (a)(i) and anamplification oligomer as specified in (a)(ii). In some suchembodiments, the amplification oligomer of (a)(i) comprises atarget-hybridizing sequence selected from SEQ ID NO:33, SEQ ID NO:34,SEQ ID NO:35, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65,and SEQ ID NO:66, including RNA equivalents and DNA/RNA chimericsthereof. In certain preferred variations, the amplification oligomer of(a)(i) comprises a target-hybridizing sequence selected from SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66, including RNAequivalents and DNA/RNA chimerics thereof.

In certain embodiments comprising an amplification oligomer as specifiedin (a)(i) and an amplification oligomer as specified in (a)(ii), theamplification oligomer of (a)(ii) comprises a target-hybridizingsequence selected from SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ IDNO:32, SEQ ID NO:52, SEQ ID NO:53, and SEQ ID NO:54, including RNAequivalents and DNA/RNA chimerics thereof. In certain preferredvariations, the amplification oligomer of (a)(ii) comprises atarget-hybridizing sequence selected from SEQ ID NO:29, SEQ ID NO:31,and SEQ ID NO:32, including RNA equivalents and DNA/RNA chimericsthereof. In particular variations, (I) the amplification oligomer of(a)(i) comprises the target-hybridizing sequence of SEQ ID NO:64, or anRNA equivalent or DNA/RNA chimeric thereof, and the amplificationoligomer of (a)(ii) comprises the target-hybridizing sequence of SEQ IDNO:29, or an RNA equivalent or DNA/RNA chimeric thereof; or (II) theamplification oligomer of (a)(i) comprises the target-hybridizingsequence of SEQ ID NO:65, or an RNA equivalent or DNA/RNA chimericthereof, and the amplification oligomer of (a)(ii) comprises thetarget-hybridizing sequence of SEQ ID NO:29 or SEQ ID NO:31, or an RNAequivalent or DNA/RNA chimeric thereof.

In some embodiments, a combination of at least two oligomers as aboveincludes a first amplification oligomer as specified in (a)(ii) and asecond amplification oligomer as specified in (a)(ii). In some suchembodiments, each of the first and second amplification oligomer as in(a)(ii) comprises a target-hybridizing sequence that is from 15 to 17nucleotides contained in the sequence of SEQ ID NO:16 and that includesat least the sequence of SEQ ID NO:27, including RNA equivalents andDNA/RNA chimerics thereof (e.g., a target-hybridizing sequence selectedfrom SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, and SEQ ID NO:32,including RNA equivalents and DNA/RNA chimerics thereof). In certainvariations, each of the first and second amplification oligomers of(a)(ii) comprises a target-hybridizing sequence of SEQ ID NO:28,including RNA equivalents and DNA/RNA chimerics thereof. In a particularvariations, the first amplification oligomer of (a)(ii) comprises thetarget hybridizing sequence of SEQ ID NO:29, or an RNA equivalent orDNA/RNA chimeric thereof, and the second amplification oligomer of(a)(ii) comprises the target hybridizing sequence of SEQ ID NO:32, or anRNA equivalent or DNA/RNA chimeric thereof.

In some embodiments of an oligomer combination as above, the combinationincludes first and second amplification oligomers as specified in (b).In some such embodiments, the first amplification oligomer of (b)comprises a target-hybridizing sequence selected from SEQ ID NO:24 andSEQ ID NO:56, including RNA equivalents and DNA/RNA chimerics thereof.In other embodiments, the first amplification oligomer of (b) comprisesa target-hybridizing sequence selected from SEQ ID NO:22, SEQ ID NO:23,SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:51, including RNA equivalentsand DNA/RNA chimerics thereof. In particular variations, (I) the firstamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric thereof, andthe second amplification oligomer of (b) comprises thetarget-hybridizing sequence of SEQ ID NO:56, or an RNA equivalent orDNA/RNA chimeric thereof; or (II) the first amplification oligomer of(b) comprises the target-hybridizing sequence of SEQ ID NO:23 or SEQ IDNO:51, or an RNA equivalent or DNA/RNA chimeric thereof, and the secondamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric thereof. Incertain variations comprising an amplification oligomer having thetarget-hybridizing sequence of SEQ ID NO:56, the nucleobase at position1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or an RNAequivalent or DNA/RNA chimeric thereof).

An oligomer combination as above may include an amplification oligomeras in (a)(i), an amplification oligomer as in (a)(ii), a firstamplification oligomer as in (b), and a second amplification oligomer asin (b). In a particular variation, the amplification oligomer of (a)(i)comprises the target-hybridizing sequence of SEQ ID NO:64, or an RNAequivalent or DNA/RNA chimeric thereof; the amplification oligomer of(a)(ii) comprises the target-hybridizing sequence of SEQ ID NO:29, or anRNA equivalent or DNA/RNA chimeric thereof; the first amplificationoligomer of (b) comprises the target-hybridizing sequence of SEQ IDNO:24, or an RNA equivalent or DNA/RNA chimeric thereof; and the secondamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:56, or an RNA equivalent or DNA/RNA chimeric thereof. Inanother variation, the amplification oligomer of (a)(i) comprises thetarget-hybridizing sequence of SEQ ID NO:29, or an RNA equivalent orDNA/RNA chimeric thereof; the amplification oligomer of (a)(ii)comprises the target-hybridizing sequence of SEQ ID NO:65; or an RNAequivalent or DNA/RNA chimeric thereof, the first amplification oligomerof (b) comprises the target-hybridizing sequence of SEQ ID NO:24; or anRNA equivalent or DNA/RNA chimeric thereof; and the second amplificationoligomer of (b) comprises the target-hybridizing sequence of SEQ IDNO:56, or an RNA equivalent or DNA/RNA chimeric thereof. In certainvariations comprising an amplification oligomer having thetarget-hybridizing sequence of SEQ ID NO:56, the nucleobase at position1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or an RNAequivalent or DNA/RNA chimeric thereof).

An oligomer combination as above may include a first amplificationoligomer as in (a)(ii), a second amplification oligomer as in (a)(ii), afirst amplification oligomer as in (b), and a second amplificationoligomer as in (b). In a particular variation, the first amplificationoligomer of (a)(ii) comprises the target-hybridizing sequence of SEQ IDNO:29, or an RNA equivalent or DNA/RNA chimeric thereof; the secondamplification oligomer of (a)(ii) comprises the target-hybridizingsequence of SEQ ID NO:32, or an RNA equivalent or DNA/RNA chimericthereof; the first amplification oligomer of (b) comprises thetarget-hybridizing sequence of SEQ ID NO:24, or an RNA equivalent orDNA/RNA chimeric thereof; and the second amplification oligomer of (b)comprises the target-hybridizing sequence of SEQ ID NO:46, or an RNAequivalent or DNA/RNA chimeric thereof.

In yet other embodiments of an oligomer combination as above, anamplification oligomer of (a) comprises a target-hybridizing sequenceselected from SEQ ID NO:29, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65,and SEQ ID NO:66, including RNA equivalents and DNA/RNA chimericsthereof, and an amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:24 and SEQ ID NO:56,including RNA equivalents and DNA/RNA chimerics thereof. In some suchembodiments, the combination includes a set of first, second, and thirdamplification oligomers comprising a set of first, second, and thirdtarget-hybridizing sequences, respectively, where the set oftarget-hybridizing sequences is selected from sets (i)-(vi) as follows:(i) SEQ ID NO:65, SEQ ID NO:29, and SEQ ID NO:24, including RNAequivalents and DNA/RNA chimerics thereof; (ii) SEQ ID NO:65, SEQ IDNO:29, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof; (iii) SEQ ID NO:29, SEQ ID NO:24, and SEQ ID NO:56, includingRNA equivalents and DNA/RNA chimerics thereof; (iv) SEQ ID NO:66, SEQ IDNO:24, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof; (v) SEQ ID NO:65, SEQ ID NO:24, and SEQ ID NO:56, including RNAequivalents and DNA/RNA chimerics thereof; and (vi) SEQ ID NO:62, SEQ IDNO:29, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof. In certain variations comprising an amplification oligomerhaving the target-hybridizing sequence of SEQ ID NO:56, the nucleobaseat position 1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or anRNA equivalent or DNA/RNA chimeric thereof).

In some embodiments, an oligomer combination as above includes a set offirst and second amplification oligomers comprising a set of first (A)and second (B) target-hybridizing sequences, respectively, where the setof target-hybridizing sequences is selected from sets (i)-(xiv) asfollows:

-   -   (i) (A) SEQ ID NO:54, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, or 51, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (ii) (A) SEQ ID NO:53, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:23, 24, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iii) (A) SEQ ID NO:52, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (iv) (A) SEQ ID NO:31, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NOs:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (v) (A) SEQ ID NO:30, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 50, or 51, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:66, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:65, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (ix) (A) SEQ ID NO:64, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (x) (A) SEQ ID NO:62, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xi) (A) SEQ ID NO:35, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xii) (A) SEQ ID NO:34, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xiii) (A) SEQ ID NO:33, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 41, 52, 44, 45, 46, or 47, or            an RNA equivalent or DNA/RNA chimeric thereof; and    -   (xiv) (A) SEQ ID NO:61, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof.            In certain embodiments comprising an amplification oligomer            having the target-hybridizing sequence of SEQ ID NO:56, the            nucleobase at position 1 of SEQ ID NO:56 is guanine (G)            (i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA            chimeric thereof). In particular variations, the set of            target-hybridizing sequences A and B is selected from sets            (i)-(xiii) as follows:    -   (i) (A) SEQ ID NO:54, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (ii) (A) SEQ ID NO:53, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (iii) (A) SEQ ID NO:31, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 45, 49, 50, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:30, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:56, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (v) (A) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 56, 48, 50, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:66, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 23, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:65, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:64, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:22, 24, 45, 56, or 50, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (ix) (A) SEQ ID NO:62, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 23, 24, 45, or 56, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (x) (A) SEQ ID NO:35, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (xi) (A) SEQ ID NO:34, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (xii) (A) SEQ ID NO:33, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof; and    -   (xiii) (A) SEQ ID NO:61, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:22, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof.

In still other embodiments, an oligomer combination as above includes aset of first and second amplification oligomers comprising a set offirst (A) and second (B) target-hybridizing sequences, respectively,where the set of target-hybridizing sequences is selected from sets(i)-(x) as follows:

-   -   (i) (A) SEQ ID NO:48, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (ii) (A) SEQ ID NO:49, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (iii) (A) SEQ ID NO:50, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:51, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (v) (A) SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 54, 61, 62, 64, 65, or            66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:22, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 54, 61, 62, 64, 65, or            66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:24, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 52, 53, 54, 61, 62,            64, 65, or 66, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (ix) (A) SEQ ID NO:56, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;            and    -   (x) (A) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof.            In certain embodiments comprising an amplification oligomer            having the target-hybridizing sequence of SEQ ID NO:56, the            nucleobase at position 1 of SEQ ID NO:56 is guanine (G)            (i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA            chimeric thereof). In particular variations, the set of            target-hybridizing sequences A and B is selected from sets            (i)-(ix) as follows:    -   (i) (A) SEQ ID NO:49, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29 or 31, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (ii) (A) SEQ ID NO:50, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29 or 31, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (iii) (A) SEQ ID NO:51, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 31, 65, or 66, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (v) (A) SEQ ID NO:22, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:31, 61, 62, 64, or 66, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:33, 34, 35, 62, 65, or 66, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:54, 62, or 64, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (viii) (A) SEQ ID NO:56, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:29, 30, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof; and    -   (ix) (A) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:31, 33, 34, 35, 53, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof.

In some embodiments of an oligomer combination as above, anamplification oligomer as in (b) is a promoter primer further includinga promoter sequence (e.g., a T7 promoter sequence) located 5′ to thetarget-hybridizing sequence. A particularly suitable promoter sequenceis a T7 promoter sequence having the sequence shown in SEQ ID NO:73.

In certain embodiments, an oligomer combination further includes atleast one detection probe oligomer. In particular embodiments, thedetection probe oligomer includes a target-hybridizing sequence that isfrom about 14 to about 28 nucleotides in length and is configured tospecifically hybridize to a target sequence contained within SEQ IDNO:39 or the complement thereof. In specific variations, the detectionprobe target-hybridizing sequence is selected from SEQ ID NO:37, SEQ IDNO:55, SEQ ID NO:67, and SEQ ID NO:71, including complements, DNAequivalents, and DNA/RNA chimerics thereof. A detection probe oligomermay contain a 2′-methoxy backbone at one or more linkages in the nucleicacid backbone.

In some variations, an oligomer combination includes at least twodetection probe oligomers. For example, an oligomer combination mayinclude at least two detection probe oligomers comprising atarget-hybridizing sequence that is from about 14 to about 28nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:39 or the complement thereof.In some such embodiments, each detection probe target-hybridizingsequence is individually selected from SEQ ID NO:37, SEQ ID NO:55, SEQID NO:67, and SEQ ID NO:71, including complements, DNA equivalents, andDNA/RNA chimerics thereof. In a specific variation, an oligomercombination includes a first detection probe oligomer comprising thetarget hybridizing sequence of SEQ ID NO:55 or its complement, or an RNAequivalent or DNA/RNA chimeric thereof, and a second detection probeoligomer comprising the target hybridizing sequence of SEQ ID NO:67 orits complement, or an RNA equivalent or DNA/RNA chimeric thereof. Inother variations, the oligomer combination includes at least threedetection probe oligomers. For example, at least three detection probeoligomers may include a first detection probe oligomer comprising thetarget hybridizing sequence of SEQ ID NO:37 or its complement, or an RNAequivalent or DNA/RNA chimeric thereof; a second detection probeoligomer comprising the target hybridizing sequence of SEQ ID NO:67 orits complement, or an RNA equivalent or DNA/RNA chimeric thereof; and athird detection probe oligomers comprising the target-hybridizingsequence of SEQ ID NO:71 or its complement, or an RNA equivalent orDNA/RNA chimeric thereof. One or more (e.g., each) of the at least twodetection probe oligomers may contain a 2′-methoxy backbone at one ormore linkages in the nucleic acid backbone.

In some embodiments, an oligomer combination further includes a captureprobe oligomer comprising a target-hybridizing sequence covalentlyattached to a sequence or moiety that binds to an immobilized probe.Particularly suitable target-hybridizing sequences include the sequencesshown in SEQ ID NO:4 and SEQ ID NO:42, including complements, DNAequivalents, and DNA/RNA chimerics thereof. In some variationscomprising a target-hybridizing sequence of SEQ ID NO:4, the nucleobaseat position 20 of SEQ ID NO:4 is adenine (A). In some such variations,the nucleobase at position 19 of SEQ ID NO:4 is cytosine (C) or uracil(U). In more specific variations, the capture probe oligomer has asequence selected from SEQ ID NO:3, SEQ ID NO:7, and SEQ ID NO:43. Incertain embodiments, an oligomer combination further includes at leasttwo or at least three capture probe oligomers as above. For example, anoligomer combination may include a first capture probe oligomercomprising the target-hybridizing sequence of SEQ ID NO:2 or itscomplement, or a DNA equivalent or DNA/RNA chimeric thereof; a secondcapture probe oligomer comprising the target-hybridizing sequence of SEQID NO:6 or its complement, or a DNA equivalent or DNA/RNA chimericthereof; and a third capture probe oligomer comprising thetarget-hybridizing sequence of SEQ ID NO:42 or its complement, or a DNAequivalent or DNA/RNA chimeric thereof. In a more particular variation,the first, second, and third capture probe oligomers respectively havethe sequences of SEQ ID NO:3, SEQ ID NO:7, and SEQ ID NO:43.

In other aspects, the present invention provides a kit or a reactionmixture comprising an oligomer combination as above.

In yet another aspect, the present invention provides a method fordetermining the presence or absence of hepatitis E virus (HEV) in asample. The method generally includes the following steps: (1)contacting a sample, suspected of containing HEV, with at least twooligomers for amplifying a target region of an HEV target nucleic acid;(2) performing an in vitro nucleic acid amplification reaction, whereany HEV target nucleic acid present in the sample is used as a templatefor generating an amplification product; and (3) detecting the presenceor absence of the amplification product, thereby determining thepresence or absence of HEV in the sample. The at least two amplificationoligomers include

-   -   (a) at least one amplification oligomer selected from (i) an        oligomer comprising a target-hybridizing sequence that is from        about 14 to about 23 contiguous nucleotides contained in the        sequence of SEQ ID NO:63 and that includes at least the sequence        of SEQ ID NO:26, including RNA equivalents and DNA/RNA chimerics        thereof, and (ii) an oligomer comprising a target-hybridizing        sequence that is from about 14 to about 23 contiguous        nucleotides contained in the sequence of SEQ ID NO:16, including        RNA equivalents and DNA/RNA chimerics thereof; and    -   (b) at least one amplification oligomer comprising a        target-hybridizing sequence that is from about 17 to about 28        contiguous nucleotides contained in the sequence of SEQ ID NO:47        and that includes at least the sequence of SEQ ID NO:25,        including RNA equivalents and DNA/RNA chimerics thereof.

Suitable amplification oligomers as specified above in (a) includeoligomers comprising a target-hybridizing sequence selected from SEQ IDNO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ IDNO:34, SEQ ID NO:35, SEQ ID NO:52, SEQ ID NO:53, SEQ ID NO:54, SEQ IDNO:61, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66,including RNA equivalents and DNA/RNA chimerics thereof. In somepreferred variations, an amplification oligomer of (a) comprises atarget-hybridizing sequence selected from SEQ ID NO:29, SEQ ID NO:31,SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:61,SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66, includingRNA equivalents and DNA/RNA chimerics thereof. In some embodiments, anamplification oligomer of (a) comprises a target-hybridizing sequencethat is from about 14 to about 20 nucleotides contained in the sequenceof SEQ ID NO:13 (e.g., SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:65, or SEQ ID NO:66).

In certain variations a method for determining the presence or absenceof HEV, an amplification oligomer as specified in (a) comprises atarget-hybridizing sequence that is from 15 to 17 nucleotides containedin the sequence of SEQ ID NO:16 and that includes at least the sequenceof SEQ ID NO:27, including RNA equivalents and DNA/RNA chimerics thereof(e.g., a target-hybridizing sequence selected from SEQ ID NO:29, SEQ IDNO:30, SEQ ID NO:31, and SEQ ID NO:32, including RNA equivalents andDNA/RNA chimerics thereof). In some embodiments, an amplificationoligomer of (a) comprises a target-hybridizing sequence of SEQ ID NO:28,including RNA equivalents and DNA/RNA chimerics thereof (e.g., atarget-hybridizing sequence selected from SEQ ID NO:29 and SEQ ID NO:32,including RNA equivalents and DNA/RNA chimerics thereof).

Suitable amplification oligomers as specified above in (b) includeoligomers comprising a target-hybridizing sequence selected from SEQ IDNO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:45, SEQ IDNO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, and SEQID NO:56, including RNA equivalents and DNA/RNA chimerics thereof. Insome preferred variations, an amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:24 and SEQ ID NO:56,including RNA equivalents and DNA/RNA chimerics thereof. In otherpreferred variations, an amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:22, SEQ ID NO:23,SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:51, including RNA equivalentsand DNA/RNA chimerics thereof. In certain variations comprising anamplification oligomer having the target-hybridizing sequence of SEQ IDNO:56, the nucleobase at position 1 of SEQ ID NO:56 is guanine (G)(i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA chimeric thereof).

In some embodiments of a method as above for determining the presence orabsence HEV, the least two amplification oligomers include anamplification oligomer as specified in (a)(i) and an amplificationoligomer as specified in (a)(ii). In some such embodiments, theamplification oligomer of (a)(i) comprises a target-hybridizing sequenceselected from SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:61,SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66, includingRNA equivalents and DNA/RNA chimerics thereof. In certain preferredvariations, the amplification oligomer of (a)(i) comprises atarget-hybridizing sequence selected from SEQ ID NO:62, SEQ ID NO:64,SEQ ID NO:65, and SEQ ID NO:66, including RNA equivalents and DNA/RNAchimerics thereof.

In certain embodiments of the method in which an amplification oligomeras specified in (a)(i) and an amplification oligomer as specified in(a)(ii) are used for amplification of the HEV target region, theamplification oligomer of (a)(ii) comprises a target-hybridizingsequence selected from SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ IDNO:32, SEQ ID NO:52, SEQ ID NO:53, and SEQ ID NO:54, including RNAequivalents and DNA/RNA chimerics thereof. In certain preferredvariations, the amplification oligomer of (a)(ii) comprises atarget-hybridizing sequence selected from SEQ ID NO:29, SEQ ID NO:31,and SEQ ID NO:32, including RNA equivalents and DNA/RNA chimericsthereof. In particular variations, (I) the amplification oligomer of(a)(i) comprises the target-hybridizing sequence of SEQ ID NO:64, or anRNA equivalent or DNA/RNA chimeric thereof, and the amplificationoligomer of (a)(ii) comprises the target-hybridizing sequence of SEQ IDNO:29, or an RNA equivalent or DNA/RNA chimeric thereof; or (II) theamplification oligomer of (a)(i) comprises the target-hybridizingsequence of SEQ ID NO:65, or an RNA equivalent or DNA/RNA chimericthereof, and the amplification oligomer of (a)(ii) comprises thetarget-hybridizing sequence of SEQ ID NO:29 or SEQ ID NO:31, or an RNAequivalent or DNA/RNA chimeric thereof.

In some embodiments of a method as above for determining the presence orabsence HEV, a combination of at least two oligomers as above includes afirst amplification oligomer as specified in (a)(ii) and a secondamplification oligomer as specified in (a)(ii). In some suchembodiments, each of the first and second amplification oligomer as in(a)(ii) comprises a target-hybridizing sequence that is from 15 to 17nucleotides contained in the sequence of SEQ ID NO:16 and that includesat least the sequence of SEQ ID NO:27, including RNA equivalents andDNA/RNA chimerics thereof (e.g., a target-hybridizing sequence selectedfrom SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, and SEQ ID NO:32,including RNA equivalents and DNA/RNA chimerics thereof). In certainvariations, each of the first and second amplification oligomers of(a)(ii) comprises a target-hybridizing sequence of SEQ ID NO:28,including RNA equivalents and DNA/RNA chimerics thereof. In a particularvariations, the first amplification oligomer of (a)(ii) comprises thetarget hybridizing sequence of SEQ ID NO:29, or an RNA equivalent orDNA/RNA chimeric thereof, and the second amplification oligomer of(a)(ii) comprises the target hybridizing sequence of SEQ ID NO:32, or anRNA equivalent or DNA/RNA chimeric thereof.

In some embodiments of a method as above, the amplifying step utilizesfirst and second amplification oligomers as specified in (b). In somesuch embodiments, the first amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:24 and SEQ ID NO:56,including RNA equivalents and DNA/RNA chimerics thereof. In otherembodiments, the first amplification oligomer of (b) comprises atarget-hybridizing sequence selected from SEQ ID NO:22, SEQ ID NO:23,SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:51, including RNA equivalentsand DNA/RNA chimerics thereof. In particular variations, (I) the firstamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric thereof, andthe second amplification oligomer of (b) comprises thetarget-hybridizing sequence of SEQ ID NO:56, or an RNA equivalent orDNA/RNA chimeric thereof; or (II) the first amplification oligomer of(b) comprises the target-hybridizing sequence of SEQ ID NO:23 or SEQ IDNO:51, or an RNA equivalent or DNA/RNA chimeric thereof, and the secondamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric thereof. Incertain variations comprising an amplification oligomer having thetarget-hybridizing sequence of SEQ ID NO:56, the nucleobase at position1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or an RNAequivalent or DNA/RNA chimeric thereof).

For amplifying the HEV target region in a method as above, anamplification oligomer as in (a)(i), an amplification oligomer as in(a)(ii), a first amplification oligomer as in (b), and a secondamplification oligomer as in (b) may be used. In a particular variation,the amplification oligomer of (a)(i) comprises the target-hybridizingsequence of SEQ ID NO:64, or an RNA equivalent or DNA/RNA chimericthereof; the amplification oligomer of (a)(ii) comprises thetarget-hybridizing sequence of SEQ ID NO:29, or an RNA equivalent orDNA/RNA chimeric thereof; the first amplification oligomer of (b)comprises the target-hybridizing sequence of SEQ ID NO:24, or an RNAequivalent or DNA/RNA chimeric thereof; and the second amplificationoligomer of (b) comprises the target-hybridizing sequence of SEQ IDNO:56, or an RNA equivalent or DNA/RNA chimeric thereof. In anothervariation, the amplification oligomer of (a)(i) comprises thetarget-hybridizing sequence of SEQ ID NO:29, or an RNA equivalent orDNA/RNA chimeric thereof; the amplification oligomer of (a)(ii)comprises the target-hybridizing sequence of SEQ ID NO:65; or an RNAequivalent or DNA/RNA chimeric thereof, the first amplification oligomerof (b) comprises the target-hybridizing sequence of SEQ ID NO:24; or anRNA equivalent or DNA/RNA chimeric thereof; and the second amplificationoligomer of (b) comprises the target-hybridizing sequence of SEQ IDNO:56, or an RNA equivalent or DNA/RNA chimeric thereof. In certainvariations comprising an amplification oligomer having thetarget-hybridizing sequence of SEQ ID NO:56, the nucleobase at position1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or an RNAequivalent or DNA/RNA chimeric thereof).

In other embodiments for amplifying the HEV target region in a method asabove, a first amplification oligomer as in (a)(ii), a secondamplification oligomer as in (a)(ii), a first amplification oligomer asin (b), and a second amplification oligomer as in (b) may be used. In aparticular variation, the first amplification oligomer of (a)(ii)comprises the target-hybridizing sequence of SEQ ID NO:29, or an RNAequivalent or DNA/RNA chimeric thereof; the second amplificationoligomer of (a)(ii) comprises the target-hybridizing sequence of SEQ IDNO:32, or an RNA equivalent or DNA/RNA chimeric thereof; the firstamplification oligomer of (b) comprises the target-hybridizing sequenceof SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric thereof; andthe second amplification oligomer of (b) comprises thetarget-hybridizing sequence of SEQ ID NO:46, or an RNA equivalent orDNA/RNA chimeric thereof.

In yet other embodiments of a method for determining the presence orabsence of HEV as above, an amplification oligomer of (a) comprises atarget-hybridizing sequence selected from SEQ ID NO:29, SEQ ID NO:62,SEQ ID NO:64, SEQ ID NO:65, and SEQ ID NO:66, including RNA equivalentsand DNA/RNA chimerics thereof, and an amplification oligomer of (b)comprises a target-hybridizing sequence selected from SEQ ID NO:24 andSEQ ID NO:56, including RNA equivalents and DNA/RNA chimerics thereof.In some such embodiments, the amplifying step uses an oligomercombination that includes a set of first, second, and thirdamplification oligomers comprising a set of first, second, and thirdtarget-hybridizing sequences, respectively, where the set oftarget-hybridizing sequences is selected from sets (i)-(vi) as follows:(i) SEQ ID NO:65, SEQ ID NO:29, and SEQ ID NO:24, including RNAequivalents and DNA/RNA chimerics thereof; (ii) SEQ ID NO:65, SEQ IDNO:29, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof; (iii) SEQ ID NO:29, SEQ ID NO:24, and SEQ ID NO:56, includingRNA equivalents and DNA/RNA chimerics thereof; (iv) SEQ ID NO:66, SEQ IDNO:24, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof; (v) SEQ ID NO:65, SEQ ID NO:24, and SEQ ID NO:56, including RNAequivalents and DNA/RNA chimerics thereof; and (vi) SEQ ID NO:62, SEQ IDNO:29, and SEQ ID NO:56, including RNA equivalents and DNA/RNA chimericsthereof. In certain variations comprising an amplification oligomerhaving the target-hybridizing sequence of SEQ ID NO:56, the nucleobaseat position 1 of SEQ ID NO:56 is guanine (G) (i.e., SEQ ID NO:46, or anRNA equivalent or DNA/RNA chimeric thereof).

In some embodiments, the amplifying step uses an oligomer combinationthat includes a set of first and second amplification oligomerscomprising a set of first (A) and second (B) target-hybridizingsequences, respectively, where the set of target-hybridizing sequencesis selected from sets (i)-(xiv) as follows:

-   -   (i) (A) SEQ ID NO:54, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, or 51, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (ii) (A) SEQ ID NO:53, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:23, 24, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iii) (A) SEQ ID NO:52, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (iv) (A) SEQ ID NO:31, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NOs:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (v) (A) SEQ ID NO:30, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 50, or 51, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:66, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:65, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (ix) (A) SEQ ID NO:64, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (x) (A) SEQ ID NO:62, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xi) (A) SEQ ID NO:35, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xii) (A) SEQ ID NO:34, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (xiii) (A) SEQ ID NO:33, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof; and    -   (xiv) (A) SEQ ID NO:61, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 22, 23, 24, 45, 56, 48, 49, 50, or 51, or            an RNA equivalent or DNA/RNA chimeric thereof.            In certain embodiments comprising an amplification oligomer            having the target-hybridizing sequence of SEQ ID NO:56, the            nucleobase at position 1 of SEQ ID NO:56 is guanine (G)            (i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA            chimeric thereof). In particular variations, the set of            target-hybridizing sequences A and B is selected from sets            (i)-(xiii) as follows:    -   (i) (A) SEQ ID NO:54, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (ii) (A) SEQ ID NO:53, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (iii) (A) SEQ ID NO:31, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 45, 49, 50, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:30, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:56, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (v) (A) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:21, 56, 48, 50, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:66, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 23, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:65, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, 56, or 51, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:64, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:22, 24, 45, 56, or 50, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (ix) (A) SEQ ID NO:62, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:22, 23, 24, 45, or 56, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (x) (A) SEQ ID NO:35, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (xi) (A) SEQ ID NO:34, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (xii) (A) SEQ ID NO:33, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:23, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof; and    -   (xiii) (A) SEQ ID NO:61, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:22, 45, or 56, or an RNA equivalent or DNA/RNA            chimeric thereof.

In still other embodiments, the amplifying step uses an oligomercombination that includes a set of first and second amplificationoligomers comprising a set of first (A) and second (B)target-hybridizing sequences, respectively, where the set oftarget-hybridizing sequences is selected from sets (i)-(x) as follows:

-   -   (i) (A) SEQ ID NO:48, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (ii) (A) SEQ ID NO:49, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (iii) (A) SEQ ID NO:50, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 31, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:51, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (v) (A) SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 54, 61, 62, 64, 65, or            66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:22, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 54, 61, 62, 64, 65, or            66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;    -   (viii) (A) SEQ ID NO:24, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 52, 53, 54, 61, 62,            64, 65, or 66, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (ix) (A) SEQ ID NO:56, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof;            and    -   (x) (A) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 30, 31, 33, 34, 35, 53, 54, 61, 62, 64,            65, or 66, or an RNA equivalent or DNA/RNA chimeric thereof.            In certain embodiments comprising an amplification oligomer            having the target-hybridizing sequence of SEQ ID NO:56, the            nucleobase at position 1 of SEQ ID NO:56 is guanine (G)            (i.e., SEQ ID NO:46, or an RNA equivalent or DNA/RNA            chimeric thereof). In particular variations, the set of            target-hybridizing sequences A and B is selected from sets            (i)-(ix) as follows:    -   (i) (A) SEQ ID NO:49, including RNA equivalents and DNA/RNA        chimerics thereof, and        -   (B) SEQ ID NO:29 or 31, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (ii) (A) SEQ ID NO:50, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29 or 31, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (iii) (A) SEQ ID NO:51, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, 31, 65, or 66, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (iv) (A) SEQ ID NO:21, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:29, or an RNA equivalent or DNA/RNA chimeric            thereof;    -   (v) (A) SEQ ID NO:22, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:31, 61, 62, 64, or 66, or an RNA equivalent or            DNA/RNA chimeric thereof;    -   (vi) (A) SEQ ID NO:23, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:33, 34, 35, 62, 65, or 66, or an RNA            equivalent or DNA/RNA chimeric thereof;    -   (vii) (A) SEQ ID NO:24, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:54, 62, or 64, or an RNA equivalent or DNA/RNA            chimeric thereof;    -   (viii) (A) SEQ ID NO:56, or an RNA equivalent or DNA/RNA        chimeric thereof, and        -   (B) SEQ ID NO:29, 30, 33, 34, 35, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof; and    -   (ix) (A) SEQ ID NO:45, or an RNA equivalent or DNA/RNA chimeric        thereof, and        -   (B) SEQ ID NO:31, 33, 34, 35, 53, 61, 62, 64, 65, or 66, or            an RNA equivalent or DNA/RNA chimeric thereof.

In some embodiments of a method for determining the presence or absenceof HEV as above, an amplification oligomer as in (b) is a promoterprimer further including a promoter sequence (e.g., a T7 promotersequence) located 5′ to the target-hybridizing sequence. A particularlysuitable promoter sequence is a T7 promoter sequence having the sequenceshown in SEQ ID NO:73.

Typically, the method for determining the presence or absence of HEVfurther includes purifying the HEV target nucleic acid from othercomponents in the sample before the amplification step (1). Inparticular embodiments, the purifying step includes contacting thesample with at least one capture probe oligomer comprising atarget-hybridizing sequence covalently attached to a sequence or moietythat binds to an immobilized probe. Particularly suitabletarget-hybridizing sequences include the sequences shown in SEQ ID NO:4and SEQ ID NO:42, including complements, DNA equivalents, and DNA/RNAchimerics thereof. In some variations of the method comprising the useof a target-hybridizing sequence of SEQ ID NO:4, the nucleobase atposition 20 of SEQ ID NO:4 is adenine (A). In some such variations, thenucleobase at position 19 of SEQ ID NO:4 is cytosine (C) or uracil (U).In more specific variations, the capture probe oligomer has a sequenceselected from SEQ ID NO:3, SEQ ID NO:7, and SEQ ID NO:43. In certainembodiments, the purifying step includes the use of at least two or atleast three capture probe oligomers as above. For example, the purifyingstep may include using a first capture probe oligomer comprising thetarget-hybridizing sequence of SEQ ID NO:2 or its complement, or a DNAequivalent or DNA/RNA chimeric thereof; a second capture probe oligomercomprising the target-hybridizing sequence of SEQ ID NO:6 or itscomplement, or a DNA equivalent or DNA/RNA chimeric thereof; and a thirdcapture probe oligomer comprising the target-hybridizing sequence of SEQID NO:42 or its complement, or a DNA equivalent or DNA/RNA chimericthereof. In a more particular variation, the first, second, and thirdcapture probe oligomers respectively have the sequences of SEQ ID NO:3,SEQ ID NO:7, and SEQ ID NO:43.

In some embodiments, the detecting step (3) includes contacting the invitro nucleic acid amplification reaction with at least one detectionprobe oligomer configured to specifically hybridize to the amplificationproduct under conditions whereby the presence or absence of theamplification product is determined, thereby determining the presence orabsence of HEV in the sample. In particular embodiments, the detectionprobe oligomer includes a target-hybridizing sequence that is from about14 to about 28 nucleotides in length and is configured to specificallyhybridize to a target sequence contained within SEQ ID NO:39 or thecomplement thereof. In specific variations, the detection probetarget-hybridizing sequence is selected from SEQ ID NO:37, SEQ ID NO:55,SEQ ID NO:67, and SEQ ID NO:71, including complements, DNA equivalents,and DNA/RNA chimerics thereof. A detection probe oligomer may contain a2′-methoxy backbone at one or more linkages in the nucleic acidbackbone.

In some variations, the detecting step includes contacting the in vitronucleic acid amplification reaction with at least two detection probeoligomers. For example, the in vitro nucleic acid amplification reactionmay be contacted with at least two detection probe oligomers comprisinga target-hybridizing sequence that is from about 14 to about 28nucleotides in length and is configured to specifically hybridize to atarget sequence contained within SEQ ID NO:39 or the complement thereof.In some such embodiments, each detection probe target-hybridizingsequence is individually selected from SEQ ID NO:37, SEQ ID NO:55, SEQID NO:67, and SEQ ID NO:71, including complements, DNA equivalents, andDNA/RNA chimerics thereof. In a specific variation, the detecting stepincludes contacting the in vitro nucleic acid amplification reactionwith a first detection probe oligomer comprising the target hybridizingsequence of SEQ ID NO:55 or its complement, or an RNA equivalent orDNA/RNA chimeric thereof, and a second detection probe oligomercomprising the target hybridizing sequence of SEQ ID NO:67 or itscomplement, or an RNA equivalent or DNA/RNA chimeric thereof. In othervariations, the detecting step includes contacting the in vitro nucleicacid amplification reaction with at least three detection probeoligomers. The at least three detection probe oligomers may include afirst detection probe oligomer comprising the target hybridizingsequence of SEQ ID NO:37 or its complement, or an RNA equivalent orDNA/RNA chimeric thereof; a second detection probe oligomer comprisingthe target hybridizing sequence of SEQ ID NO:67 or its complement, or anRNA equivalent or DNA/RNA chimeric thereof; and a third detection probeoligomers comprising the target-hybridizing sequence of SEQ ID NO:71 orits complement, or an RNA equivalent or DNA/RNA chimeric thereof. One ormore (e.g., each) of the at least two detection probe oligomers maycontain a 2′-methoxy backbone at one or more linkages in the nucleicacid backbone.

In some embodiments of a method utilizing a detection probe oligomer,the detection probe includes at least one label. In specific variations,the one or more label(s) are selected from a chemiluminescent label, afluorescent label, a quencher, or any combination thereof. In certainembodiments, the detecting step (3) detects hybridization of the atleast one labeled detection probe oligomer to the amplification productin a homogeneous detection system. A particularly suitable label for usein a homogeneous detection system is a chemiluminescent acridinium ester(AE) compound linked between two nucleobases of the at least onedetection probe oligomer.

In certain variations of a method for determining the presence orabsence of HEV as above, the amplification reaction at step (2) is anisothermal amplification reaction such as, for example, atranscription-mediated amplification (TMA) reaction.

These and other aspects of the invention will become evident uponreference to the following detailed description of the invention and theattached drawings.

Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art pertinent to the methods and compositions described. As usedherein, the following terms and phrases have the meanings ascribed tothem unless specified otherwise.

The terms “a,” “an,” and “the” include plural referents, unless thecontext clearly indicates otherwise. For example, “a nucleic acid” asused herein is understood to represent one or more nucleic acids. Assuch, the terms “a” (or “an”), “one or more,” and “at least one” can beused interchangeably herein.

“Sample” includes any specimen that may contain hepatitis E virus (HEV)(including, e.g., any one of HEV genotypes 1, 2, 3, or 4) or componentsthereof, such as nucleic acids or fragments of nucleic acids. Samplesinclude “biological samples” which include any tissue or materialderived from a living or dead human that may contain HEV or targetnucleic acid derived therefrom, including, e.g., peripheral blood,plasma, serum, lymph node, gastrointestinal tissue (e.g., liver), orother body fluids or materials. The biological sample may be treated tophysically or mechanically disrupt tissue or cell structure, thusreleasing intracellular components into a solution which may furthercontain enzymes, buffers, salts, detergents and the like, which are usedto prepare, using standard methods, a biological sample for analysis.Also, samples may include processed samples, such as those obtained frompassing samples over or through a filtering device, or followingcentrifugation, or by adherence to a medium, matrix, or support.

“Nucleic acid” refers to a multimeric compound comprising two or morecovalently bonded nucleosides or nucleoside analogs having nitrogenousheterocyclic bases, or base analogs, where the nucleosides are linkedtogether by phosphodiester bonds or other linkages to form apolynucleotide. Nucleic acids include RNA, DNA, or chimeric DNA-RNApolymers or oligonucleotides, and analogs thereof. A nucleic acid“backbone” may be made up of a variety of linkages, including one ormore of sugar-phosphodiester linkages, peptide-nucleic acid bonds (in“peptide nucleic acids” or PNAs, see, e.g., International PatentApplication Pub. No. WO 95/32305), phosphorothioate linkages,methylphosphonate linkages, or combinations thereof. Sugar moieties ofthe nucleic acid may be either ribose or deoxyribose, or similarcompounds having known substitutions such as, for example, 2′-methoxysubstitutions and 2′-halide substitutions (e.g., 2′-F). Nitrogenousbases may be conventional bases (A, G, C, T, U), analogs thereof (e.g.,inosine, 5-methylisocytosine, isoguanine; see, e.g., The Biochemistry ofthe Nucleic Acids 5-36, Adams et al., ed., 11th ed., 1992; Abraham etal., 2007, BioTechniques 43: 617-24), which include derivatives ofpurine or pyrimidine bases (e.g., N⁴-methyl deoxygaunosine, deaza- oraza-purines, deaza- or aza-pyrimidines, pyrimidine bases havingsubstituent groups at the 5 or 6 position, purine bases having analtered or replacement substituent at the 2, 6 and/or 8 position, suchas 2-amino-6-methylaminopurine, 0⁶-methylguanine, 4-thio-pyrimidines,4-amino-pyrimidines, 4-dimethylhydrazine-pyrimidines, and0⁴-alkyl-pyrimidines, and pyrazolo-compounds, such as unsubstituted or3-substituted pyrazolo[3,4-d]pyrimidine; U.S. Pat. Nos. 5,378,825,6,949,367 and International Patent Application Pub. No. WO 93/13121,each incorporated by reference herein). Nucleic acids may include“abasic” residues in which the backbone does not include a nitrogenousbase for one or more residues (see, e.g., U.S. Pat. No. 5,585,481,incorporated by reference herein). A nucleic acid may comprise onlyconventional sugars, bases, and linkages as found in RNA and DNA, or mayinclude conventional components and substitutions (e.g., conventionalbases linked by a 2′-methoxy backbone, or a nucleic acid including amixture of conventional bases and one or more base analogs). Nucleicacids may include “locked nucleic acids” (LNA), in which one or morenucleotide monomers have a bicyclic furanose unit locked in an RNAmimicking sugar conformation, which enhances hybridization affinitytoward complementary sequences in single-stranded RNA (ssRNA),single-stranded DNA (ssDNA), or double-stranded DNA (dsDNA) (Vester etal., Biochemistry 43:13233-41, 2004, incorporated by reference herein).Nucleic acids may include modified bases to alter the function orbehavior of the nucleic acid, e.g., addition of a 3′-terminaldideoxynucleotide to block additional nucleotides from being added tothe nucleic acid. Synthetic methods for making nucleic acids in vitroare well-known in the art although nucleic acids may be purified fromnatural sources using routine techniques.

The term “polynucleotide” as used herein denotes a nucleic acid chain.Throughout this application, nucleic acids are designated by the5′-terminus to the 3′-terminus. Synthetic nucleic acids, e.g., DNA, RNA,DNA/RNA chimerics, (including when non-natural nucleotides or analoguesare included therein), are typically synthesized “3′-to-5′,” i.e., bythe addition of nucleotides to the 5′-terminus of a growing nucleicacid.

A “nucleotide” as used herein is a subunit of a nucleic acid consistingof a phosphate group, a 5-carbon sugar, and a nitrogenous base (alsoreferred to herein as “nucleobase”). The 5-carbon sugar found in RNA isribose. In DNA, the 5-carbon sugar is 2′-deoxyribose. The term alsoincludes analogs of such subunits, such as a methoxy group at the 2′position of the ribose (also referred to herein as “2′-O-Me” or“2′-methoxy”). As used herein, methoxy oligonucleotides containing “T”residues have a methoxy group at the 2′ position of the ribose moiety,and a uracil at the base position of the nucleotide.

A “non-nucleotide unit” as used herein is a unit that does notsignificantly participate in hybridization of a polymer. Such units mustnot, for example, participate in any significant hydrogen bonding with anucleotide, and would exclude units having as a component one of thefive nucleotide bases or analogs thereof.

A “target nucleic acid” as used herein is a nucleic acid comprising atarget sequence to be amplified. Target nucleic acids may be DNA or RNAas described herein, and may be either single-stranded ordouble-stranded. The target nucleic acid may include other sequencesbesides the target sequence, which may not be amplified.

The term “target sequence” as used herein refers to the particularnucleotide sequence of the target nucleic acid that is to be amplifiedand/or detected. The “target sequence” includes the complexing sequencesto which oligonucleotides (e.g., priming oligonucleotides and/orpromoter oligonucleotides) complex during an amplification processes(e.g., TMA). Where the target nucleic acid is originallysingle-stranded, the term “target sequence” will also refer to thesequence complementary to the “target sequence” as present in the targetnucleic acid. Where the target nucleic acid is originallydouble-stranded, the term “target sequence” refers to both the sense (+)and antisense (−) strands.

“Target-hybridizing sequence” is used herein to refer to the portion ofan oligomer that is configured to hybridize with a target nucleic acidsequence. Preferably, the target-hybridizing sequences are configured tospecifically hybridize with a target nucleic acid sequence.Target-hybridizing sequences may be 100% complementary to the portion ofthe target sequence to which they are configured to hybridize, but notnecessarily. Target-hybridizing sequences may also include inserted,deleted and/or substituted nucleotide residues relative to a targetsequence. Less than 100% complementarity of a target-hybridizingsequence to a target sequence may arise, for example, when the targetnucleic acid is a plurality strains within a species, such as would bethe case for an oligomer configured to hybridize to various genotypes ofHEV. It is understood that other reasons exist for configuring atarget-hybridizing sequence to have less than 100% complementarity to atarget nucleic acid.

The term “targets a sequence” as used herein in reference to a region ofHEV nucleic acid refers to a process whereby an oligonucleotidehybridizes to the target sequence in a manner that allows foramplification and detection as described herein. In one preferredembodiment, the oligonucleotide is complementary with the targeted HEVnucleic acid sequence and contains no mismatches. In another preferredembodiment, the oligonucleotide is complementary but contains 1, 2, 3,4, or 5 mismatches with the targeted HEV nucleic acid sequence.Preferably, the oligonucleotide that hybridizes to the HEV nucleic acidsequence includes at least 10 to as many as 50 nucleotides complementaryto the target sequence. It is understood that at least 10 and as many as50 is an inclusive range such that 10, 50 and each whole number therebetween are included. Preferably, the oligomer specifically hybridizesto the target sequence.

The term “configured to” denotes an actual arrangement of thepolynucleotide sequence configuration of a referenced oligonucleotidetarget-hybridizing sequence. For example, amplification oligomers thatare configured to generate a specified amplicon from a target sequencehave polynucleotide sequences that hybridize to the target sequence andcan be used in an amplification reaction to generate the amplicon. Alsoas an example, oligonucleotides that are configured to specificallyhybridize to a target sequence have a polynucleotide sequence thatspecifically hybridizes to the referenced sequence under stringenthybridization conditions.

The term “configured to specifically hybridize to” as used herein meansthat the target-hybridizing region of an amplification oligonucleotide,detection probe, or other oligonucleotide is designed to have apolynucleotide sequence that could target a sequence of the referencedHEV target region. Such an oligonucleotide is not limited to targetingthat sequence only, but is rather useful as a composition, in a kit, orin a method for targeting a HEV target nucleic acid. The oligonucleotideis designed to function as a component of an assay for amplification anddetection of HEV from a sample, and therefore is designed to target HEVin the presence of other nucleic acids commonly found in testingsamples. “Specifically hybridize to” does not mean exclusively hybridizeto, as some small level of hybridization to non-target nucleic acids mayoccur, as is understood in the art. Rather, “specifically hybridize to”means that the oligonucleotide is configured to function in an assay toprimarily hybridize the target so that an accurate detection of targetnucleic acid in a sample can be determined.

The term “fragment,” as used herein in reference to the HEV targetednucleic acid, refers to a piece of contiguous nucleic acid. In certainembodiments, the fragment includes contiguous nucleotides from an HEVRNA corresponding to SEQ IN NO:1, wherein the number of contiguousnucleotides in the fragment are less than that for the entire sequencecorresponding to SEQ ID NO:1.

The term “region,” as used herein, refers to a portion of a nucleic acidwherein said portion is smaller than the entire nucleic acid. Forexample, when the nucleic acid in reference is an oligonucleotidepromoter primer, the term “region” may be used refer to the smallerpromoter portion of the entire oligonucleotide. Similarly, and also asexample only, when the nucleic acid is an HEV RNA, the term “region” maybe used to refer to a smaller area of the nucleic acid, wherein thesmaller area is targeted by one or more oligonucleotides of theinvention. As another non-limiting example, when the nucleic acid inreference is an amplicon, the term region may be used to refer to thesmaller nucleotide sequence identified for hybridization by thetarget-hybridizing sequence of a probe.

The interchangeable terms “oligomer,” “oligo,” and “oligonucleotide”refer to a nucleic acid having generally less than 1,000 nucleotide (nt)residues, including polymers in a range having a lower limit of about 5nt residues and an upper limit of about 500 to 900 nt residues. In someembodiments, oligonucleotides are in a size range having a lower limitof about 12 to 15 nt and an upper limit of about 50 to 600 nt, and otherembodiments are in a range having a lower limit of about 15 to 20 nt andan upper limit of about 22 to 100 nt. Oligonucleotides may be purifiedfrom naturally occurring sources or may be synthesized using any of avariety of well-known enzymatic or chemical methods. Preferably,oligonucleotides are synthesized using, for example, a DNA synthesizerand related chemistry (e.g., ABI 3900, Life Technologies, Foster City,Calif.). A synthesized amplification oligomer can, in one aspect, be anoligonucleotide synthesized using an automated synthesizer andphosphoramidite chemistry. In one aspect, the synthesizedoligonucleotide is made using phosphoramidite chemistry and the most3′-terminal hydroxyl group is covalently bound to a solid support. Solidsupports include, but are not limited to controlled pore glass (CPG) andmacroporous polystyrene (MPPS). In one aspect, the synthesizedoligonucleotide is made using phosphoramidite chemistry and thephosphoramidite building block have protective groups attached to theirfunctional groups. Reactive groups include, but are not limited to,dimethoxytrityl (DMT), t-butyldimethylsilyl) groups (TBDMS),tri-iso-propylsilyloxymethyl) group (TOM), and 2-cyanoethyl groups. Theterm oligonucleotide does not denote any particular function to thereagent; rather, it is used generically to cover all such reagentsdescribed herein. An oligonucleotide may serve various differentfunctions. For example, it may function as a primer if it is specificfor and capable of hybridizing to a complementary strand and can furtherbe extended in the presence of a nucleic acid polymerase; it mayfunction as a primer and provide a promoter if it contains a sequencerecognized by an RNA polymerase and allows for transcription (e.g., a T7Primer); and it may function to detect a target nucleic acid if it iscapable of hybridizing to the target nucleic acid, or an ampliconthereof, and further provides a detectible moiety (e.g., anacridinium-ester compound).

As used herein, an oligonucleotide “substantially corresponding to” aspecified reference nucleic acid sequence means that the oligonucleotideis sufficiently similar to the reference nucleic acid sequence such thatthe oligonucleotide has similar hybridization properties to thereference nucleic acid sequence in that it would hybridize with the sametarget nucleic acid sequence under stringent hybridization conditions.One skilled in the art will understand that “substantially correspondingoligonucleotides” can vary from a reference sequence and still hybridizeto the same target nucleic acid sequence. It is also understood that afirst nucleic acid corresponding to a second nucleic acid includes theRNA or DNA equivalent thereof as well as DNA/RNA chimerics thereof, andincludes the complements thereof, unless the context clearly dictatesotherwise. This variation from the nucleic acid may be stated in termsof a percentage of identical bases within the sequence or the percentageof perfectly complementary bases between the probe or primer and itstarget sequence. Thus, in certain embodiments, an oligonucleotide“substantially corresponds” to a reference nucleic acid sequence ifthese percentages of base identity or complementarity are from 100% toabout 80%. In preferred embodiments, the percentage is from 100% toabout 85%. In more preferred embodiments, this percentage is from 100%to about 90%; in other preferred embodiments, this percentage is from100% to about 95%. Similarly, a region of a nucleic acid or amplifiednucleic acid can be referred to herein as corresponding to a referencenucleic acid sequence. One skilled in the art will understand thevarious modifications to the hybridization conditions that might berequired at various percentages of complementarity to allowhybridization to a specific target sequence without causing anunacceptable level of non-specific hybridization.

As used herein, the phrase “or its complement, or an RNA equivalent orDNA/RNA chimeric thereof,” with reference to a DNA sequence, includes(in addition to the referenced DNA sequence) the complement of the DNAsequence, an RNA equivalent of the referenced DNA sequence, an RNAequivalent of the complement of the referenced DNA sequence, a DNA/RNAchimeric of the referenced DNA sequence, and a DNA/RNA chimeric of thecomplement of the referenced DNA sequence. Similarly, the phrase “or itscomplement, or a DNA equivalent or DNA/RNA chimeric thereof,” withreference to an RNA sequence, includes (in addition to the referencedRNA sequence) the complement of the RNA sequence, a DNA equivalent ofthe referenced RNA sequence, a DNA equivalent of the complement of thereferenced RNA sequence, a DNA/RNA chimeric of the referenced RNAsequence, and a DNA/RNA chimeric of the complement of the referenced RNAsequence.

As used herein, a “blocking moiety” is a substance used to “block” the3′-terminus of an oligonucleotide or other nucleic acid so that itcannot be efficiently extended by a nucleic acid polymerase. Oligomersnot intended for extension by a nucleic acid polymerase may include ablocker group that replaces the 3′ OH to prevent enzyme-mediatedextension of the oligomer in an amplification reaction. For example,blocked amplification oligomers and/or detection probes present duringamplification may not have functional 3′ OH and instead include one ormore blocking groups located at or near the 3′ end. In some embodimentsa blocking group near the 3′ end and may be within five residues of the3′ end and is sufficiently large to limit binding of a polymerase to theoligomer. In other embodiments a blocking group is covalently attachedto the 3′ terminus. Many different chemical groups may be used to blockthe 3′ end, e.g., alkyl groups, non-nucleotide linkers, alkane-dioldideoxynucleotide residues, and cordycepin.

An “amplification oligomer” is an oligomer, at least the 3′-end of whichis complementary to a target nucleic acid, and which hybridizes to atarget nucleic acid, or its complement, and participates in a nucleicacid amplification reaction. An example of an amplification oligomer isa “primer” that hybridizes to a target nucleic acid and contains a 3′ OHend that is extended by a polymerase in an amplification process.Another example of an amplification oligomer is an oligomer that is notextended by a polymerase (e.g., because it has a 3′ blocked end) butparticipates in or facilitates amplification. For example, the 5′ regionof an amplification oligonucleotide may include a promoter sequence thatis non-complementary to the target nucleic acid (which may be referredto as a “promoter primer” or “promoter provider”). Those skilled in theart will understand that an amplification oligomer that functions as aprimer may be modified to include a 5′ promoter sequence, and thusfunction as a promoter primer. Incorporating a 3′ blocked end furthermodifies the promoter primer, which is now capable of hybridizing to atarget nucleic acid and providing an upstream promoter sequence thatserves to initiate transcription, but does not provide a primer foroligo extension. Such a modified oligo is referred to herein as a“promoter provider” oligomer. Size ranges for amplificationoligonucleotides include those that are about 10 to about 70 nt long(not including any promoter sequence or poly-A tails) and contain atleast about 10 contiguous bases, or even at least 12 contiguous basesthat are complementary to a region of the target nucleic acid sequence(or a complementary strand thereof). The contiguous bases are at least80%, or at least 90%, or completely complementary to the target sequenceto which the amplification oligomer binds. An amplification oligomer mayoptionally include modified nucleotides or analogs, or additionalnucleotides that participate in an amplification reaction but are notcomplementary to or contained in the target nucleic acid, or templatesequence. It is understood that when referring to ranges for the lengthof an oligonucleotide, amplicon, or other nucleic acid, that the rangeis inclusive of all whole numbers (e.g., 19-25 contiguous nucleotides inlength includes 19, 20, 21, 22, 23, 24 & 25).

As used herein, a “promoter” is a specific nucleic acid sequence that isrecognized by a DNA-dependent RNA polymerase (“transcriptase”) as asignal to bind to the nucleic acid and begin the transcription of RNA ata specific site.

As used herein, a “promoter provider” or “provider” refers to anoligonucleotide comprising first and second regions, and which ismodified to prevent the initiation of DNA synthesis from its3′-terminus. The “first region” of a promoter provider oligonucleotidecomprises a base sequence that hybridizes to a DNA template, where thehybridizing sequence is situated 3′, but not necessarily adjacent to, apromoter region. The hybridizing portion of a promoter oligonucleotideis typically at least 10 nucleotides in length, and may extend up to 50or more nucleotides in length. The “second region” comprises a promotersequence for an RNA polymerase. A promoter oligonucleotide is engineeredso that it is incapable of being extended by an RNA- or DNA-dependentDNA polymerase, e.g., reverse transcriptase, preferably comprising ablocking moiety at its 3′-terminus as described above. As referred toherein, a “T7 Provider” is a blocked promoter provider oligonucleotidethat provides an oligonucleotide sequence that is recognized by T7 RNApolymerase.

A “terminating oligonucleotide” is an oligonucleotide comprising a basesequence that is substantially complementary to a sequence within thetarget nucleic acid in the vicinity of the 5′-end of the target region,so as to “terminate” primer extension of a nascent nucleic acid thatincludes a priming oligonucleotide, thereby providing a defined 3′-endfor the nascent nucleic acid strand. A terminating oligonucleotide isdesigned to hybridize to the target nucleic acid at a positionsufficient to achieve the desired 3′-end for the nascent nucleic acidstrand. The positioning of the terminating oligonucleotide is flexibledepending upon its design. A terminating oligonucleotide may be modifiedor unmodified. In certain embodiments, terminating oligonucleotides aresynthesized with at least one or more 2′-O-ME ribonucleotides. Thesemodified nucleotides have demonstrated higher thermal stability ofcomplementary duplexes. The 2′-O-ME ribonucleotides also function toincrease the resistance of oligonucleotides to exonucleases, therebyincreasing the half-life of the modified oligonucleotides. (See, e.g.,Majlessi et al., Nucleic Acids Res. 26:2224-9, 1988, incorporated byreference herein.) Other modifications as described elsewhere herein maybe utilized in addition to or in place of 2′-O-Me ribonucleotides. Forexample, a terminating oligonucleotide may comprise PNA or an LNA. (See,e.g., Petersen et al., J. Mol. Recognit. 13:44-53, 2000, incorporated byreference herein.) A terminating oligonucleotide of the presentinvention typically includes a blocking moiety at its 3′-terminus toprevent extension. A terminating oligonucleotide may also comprise aprotein or peptide joined to the oligonucleotide so as to terminatefurther extension of a nascent nucleic acid chain by a polymerase. Aterminating oligonucleotide of the present invention is typically atleast 10 bases in length, and may extend up to 15, 20, 25, 30, 35, 40,50 or more nucleotides in length. While a terminating oligonucleotidetypically or necessarily includes a 3′-blocking moiety, “3′-blocked”oligonucleotides are not necessarily terminating oligonucleotides.

“Amplification” refers to any known procedure for obtaining multiplecopies of a target nucleic acid sequence or its complement or fragmentsthereof. The multiple copies may be referred to as amplicons oramplification products. Amplification of “fragments” refers toproduction of an amplified nucleic acid that contains less than thecomplete target nucleic acid or its complement, e.g., produced by usingan amplification oligonucleotide that hybridizes to, and initiatespolymerization from, an internal position of the target nucleic acid.Known amplification methods include, for example, replicase-mediatedamplification, polymerase chain reaction (PCR), ligase chain reaction(LCR), strand-displacement amplification (SDA), andtranscription-mediated or transcription-associated amplification.Replicase-mediated amplification uses self-replicating RNA molecules,and a replicase such as QB-replicase (see, e.g., U.S. Pat. No.4,786,600, incorporated by reference herein). PCR amplification uses aDNA polymerase, pairs of primers, and thermal cycling to synthesizemultiple copies of two complementary strands of dsDNA or from a cDNA(see, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,800,159; eachincorporated by reference herein). LCR amplification uses four or moredifferent oligonucleotides to amplify a target and its complementarystrand by using multiple cycles of hybridization, ligation, anddenaturation (see, e.g., U.S. Pat. Nos. 5,427,930 and 5,516,663, eachincorporated by reference herein). SDA uses a primer that contains arecognition site for a restriction endonuclease and an endonuclease thatnicks one strand of a hemimodified DNA duplex that includes the targetsequence, whereby amplification occurs in a series of primer extensionand strand displacement steps (see, e.g., U.S. Pat. Nos. 5,422,252;5,547,861; and 5,648,211; each incorporated by reference herein).

Transcription-associated amplification” or “transcription-mediatedamplification” (TMA) refer to nucleic acid amplification that uses anRNA polymerase to produce multiple RNA transcripts from a nucleic acidtemplate. These methods generally employ an RNA polymerase, a DNApolymerase, deoxyribonucleoside triphosphates, ribonucleosidetriphosphates, and a template complementary oligonucleotide thatincludes a promoter sequence, and optionally may include one or moreother oligonucleotides. TMA methods and single-primertranscription-associated amplification methods are embodiments ofamplification methods used for detection of HEV target sequences asdescribed herein. Variations of transcription-associated amplificationare well-known in the art as previously disclosed in detail (see, e.g.,U.S. Pat. Nos. 4,868,105; 5,124,246; 5,130,238; 5,399,491; 5,437,990;5,554,516; and 7,374,885; and International Patent Application Pub. Nos.WO 88/01302; WO 88/10315; and WO 95/03430; each incorporated byreference herein). The person of ordinary skill in the art willappreciate that the disclosed compositions may be used in amplificationmethods based on extension of oligomer sequences by a polymerase.

As used herein, the term “real-time TMA” refers to single-primertranscription-mediated amplification (“TMA”) of target nucleic acid thatis monitored by real-time detection means.

The term “amplicon” or “amplification product” as used herein refers tothe nucleic acid molecule generated during an amplification procedurethat is complementary or homologous to a sequence contained within thetarget sequence. The complementary or homologous sequence of an ampliconis sometimes referred to herein as a “target-specific sequence.”Amplicons generated using the amplification oligomers of the currentinvention may comprise non-target specific sequences. Amplicons can bedouble-stranded or single-stranded and can include DNA, RNA, or both.For example, DNA-dependent RNA polymerase transcribes single-strandedamplicons from double-stranded DNA during transcription-mediatedamplification procedures. These single-stranded amplicons are RNAamplicons and can be either strand of a double-stranded complex,depending on how the amplification oligomers are configured. Thus,amplicons can be single-stranded RNA. RNA-dependent DNA polymerasessynthesize a DNA strand that is complementary to an RNA template. Thus,amplicons can be double-stranded DNA and RNA hybrids. RNA-dependent DNApolymerases often include RNase activity, or are used in conjunctionwith an RNase, which degrades the RNA strand. Thus, amplicons can besingle stranded DNA. RNA-dependent DNA polymerases and DNA-dependent DNApolymerases synthesize complementary DNA strands from DNA templates.Thus, amplicons can be double-stranded DNA. RNA-dependent RNApolymerases synthesize RNA from an RNA template. Thus, amplicons can bedouble-stranded RNA. DNA-dependent RNA polymerases synthesize RNA fromdouble-stranded DNA templates, also referred to as transcription. Thus,amplicons can be single stranded RNA. Amplicons and methods forgenerating amplicons are known to those skilled in the art. Forconvenience herein, a single strand of RNA or a single strand of DNA mayrepresent an amplicon generated by an amplification oligomer combinationof the current invention. Such representation is not meant to limit theamplicon to the representation shown. Skilled artisans in possession ofthe instant disclosure will use amplification oligomers and polymeraseenzymes to generate any of the numerous types of amplicons, all withinthe spirit and scope of the current invention.

A “non-target-specific sequence,” as is used herein refers to a regionof an oligomer sequence, wherein said region does not stably hybridizewith a target sequence under standard hybridization conditions.Oligomers with non-target-specific sequences include, but are notlimited to, promoter primers and molecular beacons. An amplificationoligomer may contain a sequence that is not complementary to the targetor template sequence; for example, the 5′ region of a primer may includea promoter sequence that is non-complementary to the target nucleic acid(referred to as a “promoter primer”). Those skilled in the art willunderstand that an amplification oligomer that functions as a primer maybe modified to include a 5′ promoter sequence, and thus function as apromoter primer. Similarly, a promoter primer may be modified by removalof, or synthesis without, a promoter sequence and still function as aprimer. A 3′ blocked amplification oligomer may provide a promotersequence and serve as a template for polymerization (referred to as a“promoter provider”). Thus, an amplicon that is generated by anamplification oligomer member such as a promoter primer will comprise atarget-specific sequence and a non-target-specific sequence.

“Detection probe,” “detection oligonucleotide,” and “detection probeoligomer” are used interchangeably to refer to a nucleic acid oligomerthat hybridizes specifically to a target sequence in a nucleic acid, orin an amplified nucleic acid, under conditions that promotehybridization to allow detection of the target sequence or amplifiednucleic acid. Detection may either be direct (e.g., a probe hybridizeddirectly to its target sequence) or indirect (e.g., a probe linked toits target via an intermediate molecular structure). Detection probesmay be DNA, RNA, analogs thereof or combinations thereof (e.g., DNA/RNAchimerics) and they may be labeled or unlabeled. Detection probes mayfurther include alternative backbone linkages such as, e.g., 2′-O-methyllinkages. A detection probe's “target sequence” generally refers to asmaller nucleic acid sequence region within a larger nucleic acidsequence that hybridizes specifically to at least a portion of a probeoligomer by standard base pairing. A detection probe may comprisetarget-specific sequences and other sequences that contribute to thethree-dimensional conformation of the probe (see, e.g., U.S. Pat. Nos.5,118,801; 5,312,728; 6,849,412; 6,835,542; 6,534,274; and 6,361,945;and US Patent Application Pub. No. 20060068417; each incorporated byreference herein).

By “stable” or “stable for detection” is meant that the temperature of areaction mixture is at least 2° C. below the melting temperature of anucleic acid duplex.

As used herein, a “label” refers to a moiety or compound joined directlyor indirectly to a probe that is detected or leads to a detectablesignal. Direct labeling can occur through bonds or interactions thatlink the label to the probe, including covalent bonds or non-covalentinteractions, e.g., hydrogen bonds, hydrophobic and ionic interactions,or formation of chelates or coordination complexes. Indirect labelingcan occur through use of a bridging moiety or “linker” such as a bindingpair member, an antibody or additional oligomer, which is eitherdirectly or indirectly labeled, and which may amplify the detectablesignal. Labels include any detectable moiety, such as a radionuclide,ligand (e.g., biotin, avidin), enzyme or enzyme substrate, reactivegroup, or chromophore (e.g., dye, particle, or bead that impartsdetectable color), luminescent compound (e.g., bioluminescent,phosphorescent, or chemiluminescent labels), or fluorophore. Labels maybe detectable in a homogeneous assay in which bound labeled probe in amixture exhibits a detectable change different from that of an unboundlabeled probe, e.g., instability or differential degradation properties.A “homogeneous detectable label” can be detected without physicallyremoving bound from unbound forms of the label or labeled probe (see,e.g., U.S. Pat. Nos. 5,283,174; 5,656,207; and 5,658,737; eachincorporated by reference herein). Labels include chemiluminescentcompounds, e.g., acridinium ester (“AE”) compounds that include standardAE and derivatives (see, e.g., U.S. Pat. Nos. 5,656,207; 5,658,737; and5,639,604; each incorporated by reference herein). Synthesis and methodsof attaching labels to nucleic acids and detecting labels are wellknown. (See, e.g., Sambrook et al., Molecular Cloning, A LaboratoryManual, 2nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Habor,N Y, 1989), Chapter 10, incorporated by reference herein. See also U.S.Pat. Nos. 5,658,737; 5,656,207; 5,547,842; 5,283,174; and 4,581,333;each incorporated by reference herein). More than one label, and morethan one type of label, may be present on a particular probe, ordetection may use a mixture of probes in which each probe is labeledwith a compound that produces a detectable signal (see, e.g., U.S. Pat.Nos. 6,180,340 and 6,350,579, each incorporated by reference herein).

“Capture probe,” “capture oligonucleotide,” and “capture probe oligomer”are used interchangeably to refer to a nucleic acid oligomer thatspecifically hybridizes to a target sequence in a target nucleic acid bystandard base pairing and joins to a binding partner on an immobilizedprobe to capture the target nucleic acid to a support. One example of acapture oligomer includes two binding regions: a sequence-binding region(e.g., target-specific portion) and an immobilized probe-binding region,usually on the same oligomer, although the two regions may be present ontwo different oligomers joined together by one or more linkers. Anotherembodiment of a capture oligomer uses a target-sequence binding regionthat includes random or non-random poly-GU, poly-GT, or poly U sequencesto bind non-specifically to a target nucleic acid and link it to animmobilized probe on a support.

As used herein, an “immobilized oligonucleotide,” “immobilized probe,”or “immobilized nucleic acid” refers to a nucleic acid binding partnerthat joins a capture oligomer to a support, directly or indirectly. Animmobilized probe joined to a support facilitates separation of acapture probe bound target from unbound material in a sample. Oneembodiment of an immobilized probe is an oligomer joined to a supportthat facilitates separation of bound target sequence from unboundmaterial in a sample. Supports may include known materials, such asmatrices and particles free in solution, which may be made ofnitrocellulose, nylon, glass, polyacrylate, mixed polymers, polystyrene,silane, polypropylene, metal, or other compositions, of which oneembodiment is magnetically attractable particles. Supports may bemonodisperse magnetic spheres (e.g., uniform size±5%), to which animmobilized probe is joined directly (via covalent linkage, chelation,or ionic interaction), or indirectly (via one or more linkers), wherethe linkage or interaction between the probe and support is stableduring hybridization conditions.

By “complementary” is meant that the nucleotide sequences of similarregions of two single-stranded nucleic acids, or two different regionsof the same single-stranded nucleic acid, have a nucleotide basecomposition that allow the single-stranded regions to hybridize togetherin a stable double-stranded hydrogen-bonded region under stringenthybridization or amplification conditions. Sequences that hybridize toeach other may be completely complementary or partially complementary tothe intended target sequence by standard nucleic acid base pairing(e.g., G:C, A:T, or A:U pairing). By “sufficiently complementary” ismeant a contiguous sequence that is capable of hybridizing to anothersequence by hydrogen bonding between a series of complementary bases,which may be complementary at each position in the sequence by standardbase pairing or may contain one or more residues, including abasicresidues, that are not complementary. Sufficiently complementarycontiguous sequences typically are at least 80%, or at least 90%,complementary to a sequence to which an oligomer is intended tospecifically hybridize. Sequences that are “sufficiently complementary”allow stable hybridization of a nucleic acid oligomer with its targetsequence under appropriate hybridization conditions, even if thesequences are not completely complementary. When a contiguous sequenceof nucleotides of one single-stranded region is able to form a series of“canonical” hydrogen-bonded base pairs with an analogous sequence ofnucleotides of the other single-stranded region, such that A is pairedwith U or T and C is paired with G, the nucleotides sequences are“completely” complementary (see, e.g., Sambrook et al., MolecularCloning, A Laboratory Manual, 2^(nd) ed. (Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1989) at §§ 1.90-1.91, 7.37-7.57,9.47-9.51 and 11.47-11.57, particularly §§ 9.50-9.51, 11.12-11.13,11.45-11.47 and 11.55-11.57, incorporated by reference herein). It isunderstood that ranges for percent identity are inclusive of all wholeand partial numbers (e.g., at least 90% includes 90, 91, 93.5, 97.687and etc.).

By “preferentially hybridize” or “specifically hybridize” is meant thatunder stringent hybridization assay conditions, probes hybridize totheir target sequences, or replicates thereof, to form stableprobe:target hybrids, while at the same time formation of stableprobe:non-target hybrids is minimized Thus, a probe hybridizes to atarget sequence or replicate thereof to a sufficiently greater extentthan to a non-target sequence, to enable one having ordinary skill inthe art to accurately detect or quantitate RNA replicates orcomplementary DNA (cDNA) of the target sequence formed during theamplification. Appropriate hybridization conditions are well-known inthe art, may be predicted based on sequence composition, or can bedetermined by using routine testing methods (see, e.g., Sambrook et al.,Molecular Cloning, A Laboratory Manual, 2^(nd) ed. (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989) at §§ 1.90-1.91,7.37-7.57, 9.47-9.51 and 11.47-11.57, particularly §§ 9.50-9.51,11.12-11.13, 11.45-11.47 and 11.55-11.57, incorporated by referenceherein).

By “nucleic acid hybrid,” “hybrid,” or “duplex” is meant a nucleic acidstructure containing a double-stranded, hydrogen-bonded region whereineach strand is complementary to the other, and wherein the region issufficiently stable under stringent hybridization conditions to bedetected by means including, but not limited to, chemiluminescent orfluorescent light detection, autoradiography, or gel electrophoresis.Such hybrids may comprise RNA:RNA, RNA:DNA, or DNA:DNA duplex molecules.

“Sample preparation” refers to any steps or method that treats a samplefor subsequent amplification and/or detection of HEV nucleic acidspresent in the sample. Samples may be complex mixtures of components ofwhich the target nucleic acid is a minority component. Samplepreparation may include any known method of concentrating components,such as microbes or nucleic acids, from a larger sample volume, such asby filtration of airborne or waterborne particles from a larger volumesample or by isolation of microbes from a sample by using standardmicrobiology methods. Sample preparation may include physical disruptionand/or chemical lysis of cellular components to release intracellularcomponents into a substantially aqueous or organic phase and removal ofdebris, such as by using filtration, centrifugation or adsorption.Sample preparation may include use of a nucleic acid oligonucleotidethat selectively or non-specifically capture a target nucleic acid andseparate it from other sample components (e.g., as described in U.S.Pat. No. 6,110,678 and International Patent Application Pub. No. WO2008/016988, each incorporated by reference herein).

“Separating” or “purifying” means that one or more components of asample are removed or separated from other sample components. Samplecomponents include target nucleic acids usually in a generally aqueoussolution phase, which may also include cellular fragments, proteins,carbohydrates, lipids, and other nucleic acids. “Separating” or“purifying” does not connote any degree of purification. Typically,separating or purifying removes at least 70%, or at least 80%, or atleast 95% of the target nucleic acid from other sample components.

As used herein, a “DNA-dependent DNA polymerase” is an enzyme thatsynthesizes a complementary DNA copy from a DNA template. Examples areDNA polymerase I from E. coli, bacteriophage T7 DNA polymerase, or DNApolymerases from bacteriophages T4, Phi-29, M2, or T5. DNA-dependent DNApolymerases may be the naturally occurring enzymes isolated frombacteria or bacteriophages or expressed recombinantly, or may bemodified or “evolved” forms which have been engineered to possesscertain desirable characteristics, e.g., thermostability, or the abilityto recognize or synthesize a DNA strand from various modified templates.All known DNA-dependent DNA polymerases require a complementary primerto initiate synthesis. It is known that under suitable conditions aDNA-dependent DNA polymerase may synthesize a complementary DNA copyfrom an RNA template. RNA-dependent DNA polymerases typically also haveDNA-dependent DNA polymerase activity.

As used herein, a “DNA-dependent RNA polymerase” or “transcriptase” isan enzyme that synthesizes multiple RNA copies from a double-stranded orpartially double-stranded DNA molecule having a promoter sequence thatis usually double-stranded. The RNA molecules (“transcripts”) aresynthesized in the 5′-to-3′ direction beginning at a specific positionjust downstream of the promoter. Examples of transcriptases are theDNA-dependent RNA polymerase from E. coli and bacteriophages T7, T3, andSP6.

As used herein, an “RNA-dependent DNA polymerase” or “reversetranscriptase” (“RT”) is an enzyme that synthesizes a complementary DNAcopy from an RNA template. All known reverse transcriptases also havethe ability to make a complementary DNA copy from a DNA template; thus,they are both RNA- and DNA-dependent DNA polymerases. RTs may also havean RNAse H activity. A primer is required to initiate synthesis withboth RNA and DNA templates.

As used herein, a “selective RNAse” is an enzyme that degrades the RNAportion of an RNA:DNA duplex but not single-stranded RNA,double-stranded RNA or DNA. An exemplary selective RNAse is RNAse H.Enzymes possessing the same or similar activity as RNAse H may also beused. Selective RNAses may be endonucleases or exonucleases. Mostreverse transcriptase enzymes contain an RNAse H activity in addition totheir polymerase activities. However, other sources of the RNAse H areavailable without an associated polymerase activity. The degradation mayresult in separation of RNA from a RNA:DNA complex. Alternatively, aselective RNAse may simply cut the RNA at various locations such thatportions of the RNA melt off or permit enzymes to unwind portions of theRNA. Other enzymes that selectively degrade RNA target sequences or RNAproducts of the present invention will be readily apparent to those ofordinary skill in the art.

The term “specificity,” in the context of an amplification and/ordetection system, is used herein to refer to the characteristic of thesystem which describes its ability to distinguish between target andnon-target sequences dependent on sequence and assay conditions. Interms of nucleic acid amplification, specificity generally refers to theratio of the number of specific amplicons produced to the number ofside-products (e.g., the signal-to-noise ratio). In terms of detection,specificity generally refers to the ratio of signal produced from targetnucleic acids to signal produced from non-target nucleic acids.

The term “sensitivity” is used herein to refer to the precision withwhich a nucleic acid amplification reaction can be detected orquantitated. The sensitivity of an amplification reaction is generally ameasure of the smallest copy number of the target nucleic acid that canbe reliably detected in the amplification system, and will depend, forexample, on the detection assay being employed, and the specificity ofthe amplification reaction, e.g., the ratio of specific amplicons toside-products.

As used herein, the term “relative light unit” (“RLU”) is an arbitraryunit of measurement indicating the relative number of photons emitted bythe sample at a given wavelength or band of wavelengths. RLU varies withthe characteristics of the detection means used for the measurement.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D illustrate a reference sequence for a hepatitis E virus(HEV) genome (SEQ ID NO:1), complete sequence found at GenBank underaccession number AB074918.2 and GI:21218075.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides compositions, kits, and methods foramplifying and detecting hepatitis C virus (HEV) nucleic acid from asample. Preferably, the samples are biological samples. Thecompositions, kits, and methods provide oligonucleotide sequences thatrecognize target sequences of the HEV genome, including target sequencesof HEV genotypes 1, 2, 3, and 4, or their complementary sequences. Sucholigonucleotides may be used as amplification oligonucleotides, whichmay include primers, promoter primers, blocked oligonucleotides, andpromoter provider oligonucleotides, whose functions have been describedpreviously (see, e.g., U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159;5,399,491; 5,554,516; 5,824,518; and 7,374,885; each incorporated byreference herein). Other oligonucleotides may be used as probes fordetecting amplified sequences of HEV, or for capture of HEV targetnucleic acid.

The methods provide for the sensitive and specific detection of HEVnucleic acids. The methods include performing a nucleic acidamplification of an HEV target region and detecting the amplifiedproduct by, for example, specifically hybridizing the amplified productwith a nucleic acid detection probe that provides a signal to indicatethe presence of HEV in the sample. The amplification step includescontacting the sample with one or more amplification oligomers specificfor a target sequence in an HEV target nucleic acid to produce anamplified product if HEV nucleic acid is present in the sample.Amplification synthesizes additional copies of the target sequence orits complement by using at least one nucleic acid polymerase and anamplification oligomer to produce the copies from a template strand(e.g., by extending the sequence from a primer using the templatestrand). One embodiment for detecting the amplified product uses ahybridizing step that includes contacting the amplified product with atleast one probe specific for a sequence amplified by the selectedamplification oligomers, e.g., a sequence contained in the targetsequence flanked by a pair of selected amplification oligomers.

The detection step may be performed using any of a variety of knowntechniques to detect a signal specifically associated with the amplifiedtarget sequence, such as, e.g., by hybridizing the amplification productwith a labeled detection probe and detecting a signal resulting from thelabeled probe. The detection step may also provide additionalinformation on the amplified sequence, such as, e.g., all or a portionof its nucleic acid base sequence. Detection may be performed after theamplification reaction is completed, or may be performed simultaneouslywith amplifying the target region, e.g., in real time. In oneembodiment, the detection step allows homogeneous detection, e.g.,detection of the hybridized probe without removal of unhybridized probefrom the mixture (see, e.g., U.S. Pat. Nos. 5,639,604 and 5,283,174,each incorporated by reference herein).

In embodiments that detect the amplified product near or at the end ofthe amplification step, a linear detection probe may be used to providea signal to indicate hybridization of the probe to the amplifiedproduct. One example of such detection uses a luminescentally labeledprobe that hybridizes to target nucleic acid. Luminescent label is thenhydrolyzed from non-hybridized probe. Detection is performed bychemiluminescence using a luminometer. (see, e.g., International PatentApplication Pub. No. WO 89/002476, incorporated by reference herein). Inother embodiments that use real-time detection, the detection probe maybe a hairpin probe such as, for example, a molecular beacon, moleculartorch, or hybridization switch probe that is labeled with a reportermoiety that is detected when the probe binds to amplified product. Suchprobes may comprise target-hybridizing sequences andnon-target-hybridizing sequences. Various forms of such probes have beendescribed previously (see, e.g., U.S. Pat. Nos. 5,118,801; 5,312,728;5,925,517; 6,150,097; 6,849,412; 6,835,542; 6,534,274; and 6,361,945;and US Patent Application Pub. Nos. 20060068417A1 and 20060194240A1;each incorporated by reference herein).

Preferred compositions of the instant invention are configured tospecifically hybridize to nucleic acid of all four major HEV genotypes(types 1, 2, 3, and 4) with minimal cross-reactivity to other, non-HEVnucleic acids suspected of being in a sample (e.g., other bloodbornepathogens). In certain variations, compositions of the invention furtherallow detection of sequences that are provisionally designated asbelonging to HEV genotype 6. In some aspects, the compositions of theinstant invention are configured to specifically hybridize to HEVnucleic acid with minimal cross-reactivity to one or more of hepatitis Cvirus (HCV), human immunodeficiency virus 1 (HIV 1), hepatitis B virus(HBV), and West Nile virus. In one aspect, the compositions of theinstant invention are part of a multiplex system that further includescomponents and methods for detecting one of more of these organisms.

In certain aspects of the invention, a combination of at least twooligomers is provided for determining the presence or absence of HEV ina sample. Typically, the oligomer combination includes at least twoamplification oligomers for amplifying a target region of an HEV targetnucleic acid corresponding to the sequence of SEQ ID NO:1. In suchembodiments, at least one amplification oligomer comprises atarget-hybridizing sequence in the sense orientation (“sense THS”) andat least one amplification oligomer comprises a target-hybridizingsequence in the antisense orientation (“antisense THS”), where the senseTHS and antisense THS are each configured to specifically hybridize toan HEV target sequence corresponding to a sequence contained within SEQID NO:1 and where the target-hybridizing sequences are selected suchthat the HEV sequence targeted by antisense THS is situated downstreamof the HEV sequence targeted by the sense THS (i.e., the at least twoamplification oligomers are situated such that they flank the targetregion to be amplified). In some variations, an oligomer combinationincludes (a)(i) an oligomer comprising a target-hybridizing sequencethat is from about 14 to about 23 contiguous nucleotides andsubstantially corresponding to, or identical to, a sequence that iscontained in the sequence of SEQ ID NO:63 and that includes at least thesequence of SEQ ID NO:26, or the complement thereof or an RNA equivalentor DNA/RNA chimeric thereof. In some variations, at least oneamplification oligomer is (a)(ii) an oligomer comprising atarget-hybridizing sequence that is from about 14 to about 23 contiguousnucleotides and substantially corresponding to, or identical to, asequence that is contained in the sequence of SEQ ID NO:16, or thecomplement thereof or an RNA equivalent or DNA/RNA chimeric thereof. Insome variations, at least one amplification oligomer is (b) an oligomercomprising a target-hybridizing sequence that is from about 17 to about28 contiguous nucleotides and substantially corresponding to, oridentical to, a sequence that is contained in the sequence of SEQ IDNO:47 and that includes at least the sequence of SEQ ID NO:25, or thecomplement thereof or an RNA equivalent or DNA/RNA chimeric thereof. Inmore specific embodiments, the at least one amplification oligomer fordetecting HEV includes providing the at least one amplification oligomerin an amplification reaction mixture. In one aspect, each of the atleast one amplification oligomers is provided in the amplificationreaction mixture at a concentration from about 4 pmoles/reaction toabout 12 pmoles/reaction (inclusive of all whole and partial numbers ofthe range (e.g., 4, 4.5, 5, 6.75, 8, 10, 10.25, 11, 12.01)). In somevariations, the at least one amplification oligomer is a plurality ofamplification oligomers, each of which are provided in the amplificationreaction mixture at equal concentrations. In some variations, the atleast one amplification oligomer is a plurality of amplificationoligomers, each of which are not necessarily provided in theamplification reaction mixture at equal concentrations (e.g., oneamplification oligomer is provided at twice the concentration of anotheramplification oligomer in an amplification reaction mixture).

In variations comprising an amplification oligomer as in (a)(i),(a)(ii), or (b) above, the oligomer combination includes at least one anamplification oligomer comprising an HEV-specific target-hybridizingsequence of the opposite polarity (sense vs. antisense or vice versa) asthe target-hybridizing sequence of the oligomer of (a)(i), (a)(ii), or(b), such that at least two amplification oligomers flank a targetregion to be amplified. In some such embodiments, an oligomercombination includes at least one oligomer as in (a)(i) and/or (a)(ii),and at least one oligomer as in (b), such that the oligomer(s) of (a)(i)and/or (a)(ii) and the oligomer(s) of (b) flank the target region to beamplified. In some such variations, the oligomer combination includes atleast one amplification oligomer as in (a)(i), at least oneamplification oligomer as in (a)(ii), and at least one amplificationoligomer (e.g., two amplification oligomers) as in (b). In other suchvariations, the oligomer combination includes at least two amplificationoligomers as in (b) and at least one amplification oligomer as in eitherof (a)(i) or (a)(ii).

In more specific embodiments of the present invention, an oligomercombination for determining the presence or absence of HEV in a sampleincludes (1) at least one amplification oligomer comprising an HEVtarget-hybridizing region substantially corresponding to at least onesense oligomer sequence depicted in Table 1 below, and (2) at least oneamplification oligomer comprising an HEV target hybridizing regionsubstantially corresponding to at least one antisense oligomer sequencedepicted in Table 1. In some such embodiments, the oligomer combinationincludes at least two amplification oligomers of (1) above and/or atleast two amplification oligomers of (2) above. In particularvariations, the sense and/or antisense target-hybridizing sequence(s) ofan amplification oligomer combination comprises or consists of the senseand/or antisense sequence(s) selected from Table 1.

TABLE 1 Exemplary Sense and Antisense AmplificationOligomer Target-hybridizing Sequences for Amplification of HEV Target Regions SEQ ID Sense/ NO: SequenceAntisense^(l) 21 AGGGGTTGGTTGGATGAATATAG Antisense 22AGGGGTTGGTTGGATGAATATAGG Antisense 23 AGGGGTTGGTTGGATGAATATAGGGAntisense 24 AGGGGTTGGTTGGATGAATATAGGGGA Antisense  28²NCGGCGGTGGTTTCTNN Sense 29 CCGGCGGTGGTTTCT Sense 30 CCGGCGGTGGTTTCTGSense 31 CCGGCGGTGGTTTCTGG Sense 32 CGGCGGTGGTTTCTGG Sense 33CTATGCTGCCCGCGCC Sense 34 CTATGCTGCCCGCGCCA Sense 35 CTATGCTGCCCGCGCCACSense 45 GGCGAAGGGGTTGGTTGGATGAA Antisense 46 GGGCGAAGGGGTTGGTTGGATGAAAntisense 47 GGTTGGTTGGATGAATATAG Antisense 49 GGTTGGTTGGATGAATATAGGAntisense 50 GGTTGGTTGGATGAATATAGGG Antisense 51GGTTGGTTGGATGAATATAGGGGA Antisense 52 GGTTTCTGGGGTGAC Sense 53GTGGTTTCTGGGGTGA Sense 54 GTGGTTTCTGGGGTGAC Sense 56SGGCGAAGGGGTTGGTTGGATGAA Antisense 61 TGCCTATGCTGCCCGCGCCAC Sense 62TGCTGCCCGCGCCA Sense 64 TGCTGCCCGCGCCAC Sense 65 TGCTGCCCGCGCCACC Sense66 TGCTGCCCGCGCCACCG Sense ¹The Sense/Antisense designation of thesesequences is for exemplary purposes only. Such designation does notnecessarily limit a sequence to the accompanying designation. ²N atposition 1 is C or is absent, N at position 16 is G or absent, and N atposition 17 is G or is absent. In some embodiments, if N at position 16is G and N at position 17 is absent, then N at position 1 is C.

In certain embodiments, an amplification oligomer as described herein isa promoter primer or promoter provider further comprising a promotersequence located 5′ to the target-hybridizing sequence and which isnon-complementary to the HEV target nucleic acid. For example, in someembodiments of an oligomer combination as described herein foramplification of an HEV target region, an amplification oligomer asdescribed above in (b) (e.g., an amplification oligomer comprising orconsisting of an antisense target-hybridizing sequence as shown inTable 1) is a promoter primer further comprising a 5′ promoter sequence.In particular embodiments, the promoter sequence is a T7 RNA polymerasepromoter sequence such as, for example, a T7 promoter sequence havingthe sequence shown in SEQ ID NO:73. In specific variations, theamplification oligomer of (b) is a promoter primer having the sequenceshown in SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ IDNO:14, SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:18, or SEQ IDNO:20.

In some embodiments, an oligomer combination as described herein furtherincludes a terminating oligonucleotide (also referred to herein as a“blocker” oligonucleotide) comprising comprises a base sequencesubstantially complementary (e.g., fully complementary) to a sequencecontained within the target nucleic acid in the vicinity of the 5′-endof the target region. A terminating oligomer is typically used incombination with, e.g., a promoter provider amplification oligomer, suchas, for example, in certain embodiments described herein relating totranscription-mediated amplification (TMA).

In some embodiments, an oligomer combination as described herein furthercomprises at least one capture probe oligomer comprising atarget-hybridizing sequence substantially corresponding to a sequencecontained in the complement of SEQ ID NO:1, wherein thetarget-hybridizing sequence is covalently attached to a sequence ormoiety that binds to an immobilized probe. In specific variations, thetarget-hybridizing sequence comprises or consists of a sequencesubstantially corresponding to, or identical to, a sequence selectedfrom SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:42, includingcomplements, DNA equivalents, and DNA/RNA chimerics thereof. In morespecific variations, the capture probe oligomer has a sequence selectedfrom SEQ ID NO:3, SEQ ID NO:7, and SEQ ID NO:43. An oligomer combinationmay include at least two (e.g., three) capture probe oligomers as above.In more specific embodiments, the at least one capture probe oligomerincludes providing the at least one capture probe oligomer in a targetcapture reaction mixture. In one aspect, each of the at least onecapture probe oligomers is provided in the target capture reactionmixture at a concentration from about 3 pmoles/reaction to about 6pmoles/reaction (inclusive of all whole and partial numbers of the range(e.g., 4, 4.75, 5.12, 5.98, 6)). When a plurality of at least onecapture probe oligomer is used in a target capture reaction theconcentration of each capture probe oligomer may be equal to theconcentration of the others or there may be varied concentrations, asdescribed herein.

In certain variations, an oligomer combination as described hereinfurther comprises at least one detection probe oligomer configured tospecifically hybridize to an HEV target sequence that is amplifiableusing the first and second amplification oligomers (e.g., an HEV targetsequence that is flanked by the target-hybridizing sequences of thefirst and second amplification oligomers). In particular embodiments,the detection probe oligomer includes a target-hybridizing sequence thatis from about 14 to about 28 nucleotides in length and is configured tospecifically hybridize to a target sequence contained within SEQ IDNO:39 or the complement thereof. Particularly suitable detection probeoligomers include, for example, oligomers comprising atarget-hybridizing sequence substantially corresponding to, or identicalto, a sequence selected from SEQ ID NO:37, SEQ ID NO:55, SEQ ID NO:67,and SEQ ID NO:71, including complements, DNA equivalents, and DNA/RNAchimerics thereof. A detection probe oligomer may contain a 2′-methoxybackbone at one or more linkages in the nucleic acid backbone. In somevariations, an oligomer combination includes at least two detectionprobe oligomers. In more specific embodiments, the at least onedetection probe oligomer includes providing the at least one detectionprobe oligomer in an amplicon detection reaction mixture. In one aspect,each of the at least one detection probe oligomers is provided in thedetection reaction mixture at about 2.0 E+06 RLU/reaction to about 6.0E+06 RLU/reaction (inclusive of all whole and partial numbers of therange (e.g., 2.0 E+06, 2.138 E+06, 3.385 E+06 RLU)). When a plurality ofat least one detection probe oligomer is used in a detection reactionthe concentration of each detection oligomer may be equal to theconcentration of the others or there may be varied concentrations, asdescribed herein.

Typically, a detection probe oligomer in accordance with the presentinvention further includes a label. Particularly suitable labels includecompounds that emit a detectable light signal, e.g., fluorophores orluminescent (e.g., chemiluminescent) compounds that can be detected in ahomogeneous mixture. More than one label, and more than one type oflabel, may be present on a particular probe, or detection may rely onusing a mixture of probes in which each probe is labeled with a compoundthat produces a detectable signal (see, e.g., U.S. Pat. Nos. 6,180,340and 6,350,579, each incorporated by reference herein). Labels may beattached to a probe by various means including covalent linkages,chelation, and ionic interactions, but preferably the label iscovalently attached. For example, in some embodiments, a detection probehas an attached chemiluminescent label such as, e.g., an acridiniumester (AE) compound (see, e.g., U.S. Pat. Nos. 5,185,439; 5,639,604;5,585,481; and 5,656,744; each incorporated by reference herein), whichin typical variations is attached to the probe by a non-nucleotidelinker (see, e.g., U.S. Pat. Nos. 5,585,481; 5,656,744; and 5,639,604,particularly at column 10, line 6 to column 11, line 3, and Example 8;each incorporated by reference herein). In other embodiments, adetection probe comprises both a fluorescent label and a quencher, acombination that is particularly useful in fluorescence resonance energytransfer (FRET) assays. Specific variations of such detection probesinclude, e.g., a TaqMan detection probe (Roche Molecular Diagnostics)and a “molecular beacon” (see, e.g., Tyagi et al., Nature Biotechnol.16:49-53, 1998; U.S. Pat. Nos. 5,118,801 and 5,312,728; eachincorporated by reference herein).

A detection probe oligomer in accordance with the present invention mayfurther include a non-target-hybridizing sequence. Specific embodimentsof such detection probes include, for example, probes that formconformations held by intramolecular hybridization, such asconformations generally referred to as hairpins. Particularly suitablehairpin probes include a “molecular torch” (see, e.g., U.S. Pat. Nos.6,849,412; 6,835,542; 6,534,274; and 6,361,945, each incorporated byreference herein) and a “molecular beacon” (see, e.g., Tyagi et al.,supra; U.S. Pat. Nos. 5,118,801 and 5,312,728, supra). Methods for usingsuch hairpin probes are well-known in the art.

In yet other embodiments, a detection probe is a linear oligomers thatdoes not substantially form conformations held by intramolecular bonds.In specific variations, a linear detection probe oligomer includes achemiluminescent compound as the label, preferably an acridinium ester(AE) compound.

In yet other variations, an oligomer combination for detection of an HEVnucleic acid further comprises a probe protection oligomer substantiallycomplementary to a detection probe oligomer. A probe protection oligomermay be hybridized to a substantially complementary, labeled detectionprobe oligomer (e.g., a probe labeled with a chemiluminescent compound)to stabilize the labeled probe during storage. In specific embodiments,a probe protection oligomer has a sequence substantially correspondingto, or identical to, a sequence selected from SEQ ID NO:36 and SEQ IDNO:40.

Also provided by the present invention are detection probe oligomers,capture probe oligomers, and probe protection oligomers as describedherein.

In another aspect, the present invention provides methods fordetermining the presence or absence of HEV in a sample using an oligomercombination as described herein. Such a method generally includes (1)contacting the sample with at least two oligomers for amplifying an HEVnucleic acid target region corresponding to an HEV target nucleic acid,where the oligomers include at least two amplification oligomers asdescribed above; (2) performing an in vitro nucleic acid amplificationreaction, where any HEV target nucleic acid present in the sample isused as a template for generating an amplification product; and (3)detecting the presence or absence of the amplification product, therebydetermining the presence or absence of HEV in the sample. A detectionmethod in accordance with the present invention typically furtherincludes the step of obtaining the sample to be contacted with the atleast two oligomers. In certain embodiments, “obtaining” a sample to beused in steps (1)-(3) includes, for example, receiving the sample at atesting facility or other location where one or more steps of the methodare performed, and/or retrieving the sample from a location (e.g., fromstorage or other depository) within a facility where one or more stepsof the method are performed.

In certain embodiments, the method further includes purifying the HEVtarget nucleic acid from other components in the sample before thecontacting step. Such purification may include methods of separatingand/or concentrating organisms contained in a sample from other samplecomponents. In particular embodiments, purifying the target nucleic acidincludes capturing the target nucleic acid to specifically ornon-specifically separate the target nucleic acid from other samplecomponents. Non-specific target capture methods may involve selectiveprecipitation of nucleic acids from a substantially aqueous mixture,adherence of nucleic acids to a support that is washed to remove othersample components, or other means of physically separating nucleic acidsfrom a mixture that contains HEV nucleic acid and other samplecomponents.

In some embodiments, an HEV target nucleic is selectively separated fromother sample components by specifically hybridizing the HEV targetnucleic acid to a capture probe oligomer. The capture probe oligomercomprises a target-hybridizing sequence configured to specificallyhybridize to an HEV target sequence so as to form atarget-sequence:capture-probe complex that is separated from samplecomponents. Suitable capture probe target-hybridizing sequences includesequences substantially corresponding to, or identical to, a sequenceselected from SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, and SEQ ID NO:42,including complements, DNA equivalents, and DNA/RNA chimerics thereof.In a preferred variation, the specific target capture binds the HEVtarget:capture-probe complex to an immobilized probe to form atarget:capture-probe:immobilized-probe complex that is separated fromthe sample and, optionally, washed to remove non-target samplecomponents (see, e.g., U.S. Pat. Nos. 6,110,678; 6,280,952; and6,534,273; each incorporated by reference herein). In such variations,the capture probe oligomer further comprises a sequence or moiety thatbinds attaches the capture probe, with its bound target sequence, to animmobilized probe attached to a solid support, thereby permitting thehybridized target nucleic acid to be separated from other samplecomponents.

In more specific embodiments, the capture probe oligomer includes a tailportion (e.g., a 3′ tail) that is not complementary to the HEV targetsequence but that specifically hybridizes to a sequence on theimmobilized probe, thereby serving as the moiety allowing the targetnucleic acid to be separated from other sample components, such aspreviously described in, e.g., U.S. Pat. No. 6,110,678, incorporatedherein by reference. Any sequence may be used in a tail region, which isgenerally about 5 to 50 nt long, and preferred embodiments include asubstantially homopolymeric tail of about 10 to 40 nt (e.g., A₁₀ toA₄₀), more preferably about 14 to 33 nt (e.g., A₁₄ to A₃₀ or T₃A₁₄ toT₃A₃₀), that bind to a complementary immobilized sequence (e.g., poly-T)attached to a solid support, e.g., a matrix or particle. For example, inspecific embodiments of a capture probe comprising a 3′ tail, thecapture probe has a sequence selected from SEQ ID NO:3, SEQ ID NO:7, andSEQ ID NO:43.

Target capture typically occurs in a solution phase mixture thatcontains one or more capture probe oligomers that hybridize specificallyto the HEV target sequence under hybridizing conditions, usually at atemperature higher than the T_(m) of thetail-sequence-immobilized-probe-sequence duplex. For embodimentscomprising a capture probe tail, the HEV-target: capture-probe complexis captured by adjusting the hybridization conditions so that thecapture probe tail hybridizes to the immobilized probe, and the entirecomplex on the solid support is then separated from other samplecomponents. The support with the attachedimmobilized-probe:capture-probe:HEV-target-sequence may be washed one ormore times to further remove other sample components. Preferredembodiments use a particulate solid support, such as paramagnetic beads,so that particles with the attachedHEV-target:capture-probeimmobilized-probe complex may be suspended in awashing solution and retrieved from the washing solution, preferably byusing magnetic attraction. To limit the number of handling steps, theHEV target nucleic acid may be amplified by simply mixing the HEV targetsequence in the complex on the support with amplification oligomers andproceeding with amplification steps.

Amplifying an HEV target sequence utilizes an in vitro amplificationreaction using at least two amplification oligomers that flank a targetregion to be amplified. In particular embodiments, the target region tobe amplified substantially corresponds to SEQ ID NO:1 from aboutnucleotide position 5230 to about nucleotide position 5379. Particularlysuitable amplification oligomer combinations for amplification of thesetarget regions are described herein (see, e.g., paragraphs [6]-[19] and[95]-[98], supra). Suitable amplification methods include, for example,replicase-mediated amplification, polymerase chain reaction (PCR),ligase chain reaction (LCR), strand-displacement amplification (SDA),and transcription-mediated or transcription-associated amplification(TMA). Such amplification methods are well-known in the art (see, e.g.,paragraphs [67] and [68], supra) and are readily used in accordance withthe methods of the present invention.

For example, some amplification methods that use TMA amplificationinclude the following steps. Briefly, the target nucleic acid thatcontains the sequence to be amplified is provided as single-strandednucleic acid (e.g., ssRNA or ssDNA). Those skilled in the art willappreciate that conventional melting of double stranded nucleic acid(e.g., dsDNA) may be used to provide single-stranded target nucleicacids. A promoter primer binds specifically to the target nucleic acidat its target sequence and a reverse transcriptase (RT) extends the 3′end of the promoter primer using the target strand as a template tocreate a cDNA copy of the target sequence strand, resulting in anRNA:DNA duplex. An RNase digests the RNA strand of the RNA:DNA duplexand a second primer binds specifically to its target sequence, which islocated on the cDNA strand downstream from the promoter primer end. RTsynthesizes a new DNA strand by extending the 3′ end of the secondprimer using the first cDNA template to create a dsDNA that contains afunctional promoter sequence. An RNA polymerase specific for thepromoter sequence then initiates transcription to produce RNAtranscripts that are about 100 to 1000 amplified copies (“amplicons”) ofthe initial target strand in the reaction. Amplification continues whenthe second primer binds specifically to its target sequence in each ofthe amplicons and RT creates a DNA copy from the amplicon RNA templateto produce an RNA:DNA duplex. RNase in the reaction mixture digests theamplicon RNA from the RNA:DNA duplex and the promoter primer bindsspecifically to its complementary sequence in the newly synthesized DNA.RT extends the 3′ end of the promoter primer to create a dsDNA thatcontains a functional promoter to which the RNA polymerase binds totranscribe additional amplicons that are complementary to the targetstrand. The autocatalytic cycles of making more amplicon copies repeatduring the course of the reaction resulting in about a billion-foldamplification of the target nucleic acid present in the sample. Theamplified products may be detected in real-time during amplification, orat the end of the amplification reaction by using a probe that bindsspecifically to a target sequence contained in the amplified products.Detection of a signal resulting from the bound probes indicates thepresence of the target nucleic acid in the sample.

In some embodiments, the method utilizes a “reverse” TMA reaction. Insuch variations, the initial or “forward” amplification oligomer is apriming oligonucleotide that hybridizes to the target nucleic acid inthe vicinity of the 3′-end of the target region. A reverse transcriptase(RT) synthesizes a cDNA strand by extending the 3′-end of the primerusing the target nucleic acid as a template. The second or “reverse”amplification oligomer is a promoter primer or promoter provider havinga target-hybridizing sequence configured to hybridize to atarget-sequence contained within the synthesized cDNA strand. Where thesecond amplification oligomer is a promoter primer, RT extends the 3′end of the promoter primer using the cDNA strand as a template to createa second, cDNA copy of the target sequence strand, thereby creating adsDNA that contains a functional promoter sequence. Amplification thencontinues essentially as described above in paragraph [113] forinitiation of transcription from the promoter sequence utilizing an RNApolymerase. Alternatively, where the second amplification oligomer is apromoter provider, a terminating oligonucleotide, which hybridizes to atarget sequence that is in the vicinity to the 5′-end of the targetregion, is typically utilized to terminate extension of the primingoligomer at the 3′-end of the terminating oligonucleotide, therebyproviding a defined 3′-end for the initial cDNA strand synthesized byextension from the priming oligomer. The target-hybridizing sequence ofthe promoter provider then hybridizes to the defined 3′-end of theinitial cDNA strand, and the 3′-end of the cDNA strand is extended toadd sequence complementary to the promoter sequence of the promoterprovider, resulting in the formation of a double-stranded promotersequence. The initial cDNA strand is then used a template to transcribemultiple RNA transcripts complementary to the initial cDNA strand, notincluding the promoter portion, using an RNA polymerase that recognizesthe double-stranded promoter and initiates transcription therefrom. Eachof these RNA transcripts is then available to serve as a template forfurther amplification from the first priming amplification oligomer.

Detection of the amplified products may be accomplished by a variety ofmethods. The nucleic acids may be associated with a surface that resultsin a physical change, such as a detectable electrical change. Amplifiednucleic acids may be detected by concentrating them in or on a matrixand detecting the nucleic acids or dyes associated with them (e.g., anintercalating agent such as ethidium bromide or cyber green), ordetecting an increase in dye associated with nucleic acid in solutionphase. Other methods of detection may use nucleic acid detection probesthat are configured to specifically hybridize to a sequence in theamplified product and detecting the presence of the probe:productcomplex, or by using a complex of probes that may amplify the detectablesignal associated with the amplified products (e.g., U.S. Pat. Nos.5,424,413; 5,451,503; and 5,849,481; each incorporated by referenceherein). Directly or indirectly labeled probes that specificallyassociate with the amplified product provide a detectable signal thatindicates the presence of the target nucleic acid in the sample. Inparticular, the amplified product will contain a target sequence in orcomplementary to a sequence in the HEV genomic RNA, and a probe willbind directly or indirectly to a sequence contained in the amplifiedproduct to indicate the presence of HEV nucleic acid in the testedsample.

Preferred embodiments of detection probes that hybridize to thecomplementary amplified sequences may be DNA or RNA oligomers, oroligomers that contain a combination of DNA and RNA nucleotides, oroligomers synthesized with a modified backbone, e.g., an oligomer thatincludes one or more 2′-methoxy substituted ribonucleotides. Probes usedfor detection of the amplified HEV sequences may be unlabeled anddetected indirectly (e.g., by binding of another binding partner to amoiety on the probe) or may be labeled with a variety of detectablelabels. Particular embodiments of detection probes suitable for use inaccordance with methods of the present invention are further describedherein (see, e.g., paragraphs [20], [21], and [39]-[41], supra). In somepreferred embodiments of the method for detecting HEV sequences, such asin certain embodiments using transcription-mediated amplification (TMA),the detection probe is a linear chemiluminescently labeled probe, morepreferably, a linear acridinium ester (AE) labeled probe.

Oligomers that are not intended to be extended by a nucleic acidpolymerase preferably include a blocker group that replaces the 3′ OH toprevent enzyme-mediated extension of the oligomer in an amplificationreaction. For example, blocked amplification oligomers and/or detectionprobes present during amplification preferably do not have a functional3′ OH and instead include one or more blocking groups located at or nearthe 3′ end. A blocking group near the 3′ end is preferably within fiveresidues of the 3′ end and is sufficiently large to limit binding of apolymerase to the oligomer, and other preferred embodiments contain ablocking group covalently attached to the 3′ terminus. Many differentchemical groups may be used to block the 3′ end, e.g., alkyl groups,non-nucleotide linkers, alkane-diol dideoxynucleotide residues, andcordycepin.

Examples of oligomers that are typically blocked at the 3′ end—and whichare particularly suitable in certain embodiments usingtranscription-mediated amplification—are promoter providers. Asdescribed previously, a promoter provider comprises firsttarget-hybridizing region and, situated 5′ to the first region, a secondregion comprising a promoter sequence for an RNA polymerase. Thepromoter provider oligonucleotide is modified to prevent the initiationof DNA synthesis from its 3′-terminus, such as by including a blockergroup as discussed above.

Another example of typically 3′-blocked oligomers are terminating(“blocker”) oligonucleotides, previously described above. A terminatingoligomer is typically used in combination with, e.g., a promoterprovider amplification oligomer, such as, for example, in certainembodiments described herein relating to transcription-mediatedamplification (TMA). A terminating oligomer hybridizes to a sequencecontained within the target nucleic acid in the vicinity of the 5′-endof the target region so as to “terminate” primer extension of a nascentnucleic acid that includes a priming oligonucleotide, thereby providinga defined 3′-end for the nascent nucleic acid strand.

Other embodiments using transcription-mediated amplification utilize apromoter primer, which comprises a first target-hybridizing region and,situated 5′ to the first region, a second region comprising a promotersequence for an RNA polymerase, but which is not modified to prevent theinitiation of DNA synthesis from its 3′-terminus. In some embodiments, apromoter primer for use in accordance with the detection methodcomprises a target-hybridizing sequence having a sequence substantiallycorresponding to, or identical to, a sequence selected from SEQ IDNO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:45, SEQ IDNO:46, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ IDNO:56. In certain variations of a promoter primer comprising atarget-hybridizing sequence as in SEQ ID NO:56, the nucleobase atposition 1 of SEQ ID NO:56 is guanine (G); in other variations, thepromoter primer has degeneracy at position 1 of SEQ ID NO:56, such thisposition is occupied by either cytosine (C) or guanine (G) within apopulation of oligomers comprising SEQ ID NO:56. In more specificvariations, a promoter primer for use in accordance with the detectionmethod has the sequence shown in SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9,SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:15,SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, or SEQ ID NO:20.

Assays for detection of the HEV nucleic acid may optionally include anon-HEV internal control (IC) nucleic acid that is amplified anddetected in the same assay reaction mixtures by using amplification anddetection oligomers specific for the IC sequence. IC nucleic acidsequences can be RNA template sequences (e.g., and in vitro transcript),synthetic nucleic acid sequences that are spiked into a sample or the ICnucleic acid sequences may be a cellular component. IC nucleic acidsequences that are cellular components can be from exogenous cellularsources or endogenous cellular sources relative to the specimen. Inthese instances, an internal control nucleic acid is co-amplified withthe HEV nucleic acid in the amplification reaction mixtures. Theinternal control amplification product and the HEV target sequenceamplification product can be detected independently. Two differentinternal control systems were employed in the procedures describedbelow.

A first arrangement for internal control systems was useful formonitoring the integrity of amplification and detection reactions thatemploy paired sets of primers and an oligonucleotide probe thathybridized amplification product at a position between the primerbinding sites, or the complements thereof. This arrangement was used inthe assays described under Examples below. In a simple application, theinternal control template nucleic acid can be distinguished from theanalyte template nucleic acid at the sequence of bases serving as theprobe binding site. These bases may be scrambled, replaced by anunrelated base sequence, or simply contain a sufficient number of pointmutations to result in differential probe binding. In this way, nucleicacid products resulting from amplification of analyte nucleic acid canbe detected by an analyte-specific probe, and not by an internalcontrol-specific probe. Likewise, amplicons resulting from amplificationof internal control nucleic acid can be detected by an internalcontrol-specific probe, and not by an analyte-specific probe. Thisconfiguration allows that both analyte and internal control nucleic acidtemplates may be amplified using identical primers, or primer sets.

In certain embodiments, amplification and detection of a signal from theamplified IC sequence demonstrates that the assay reagents, conditions,and performance of assay steps were properly used in the assay if nosignal is obtained for the intended target HEV nucleic acid (e.g.,samples that test negative for HEV). An IC may also be used as aninternal calibrator for the assay when a quantitative result is desired,i.e., the signal obtained from the IC amplification and detection isused to set a parameter used in an algorithm for quantitating the amountof HEV nucleic acid in a sample based on the signal obtained for anamplified HEV target sequence. ICs are also useful for monitoring theintegrity of one or more steps in an assay. A preferred embodiment of asynthetic IC nucleic acid sequence is a randomized sequence that hasbeen derived from a naturally occurring source (e.g., an HIV sequencethat has been rearranged in a random manner). Another preferred ICnucleic acid sequence may be an RNA transcript isolated from a naturallyoccurring source or synthesized in vitro, such as by making transcriptsfrom a cloned randomized sequence such that the number of copies of ICincluded in an assay may be accurately determined. The primers and probefor the IC target sequence are configured and synthesized by using anywell-known method provided that the primers and probe function foramplification of the IC target sequence and detection of the amplifiedIC sequence using substantially the same assay conditions used toamplify and detect the HEV target sequence. In preferred embodimentsthat include a target capture-based purification step, it is preferredthat a target capture probe specific for the IC target be included inthe assay in the target capture step so that the IC is treated in theassay in a manner analogous to that for the intended HEV analyte in allof the assay steps.

In certain embodiments of a method for determining the presence orabsence of HEV in sample, the method further includes the use of a probeprotection oligomer as described herein to adjust assay sensitivity.

Also provided by the subject invention is a reaction mixture fordetermining the presence or absence of an HEV target nucleic acid in asample. A reaction mixture in accordance with the present invention atleast comprises one or more of the following: an oligomer combination asdescribed herein for amplification of an HEV target nucleic acid; acapture probe oligomer as described herein for purifying the HEV targetnucleic acid; a detection probe oligomer as described herein fordetermining the presence or absence of an HEV amplification product; anda probe protection oligomer as described herein for detuning sensitivityof an assay for detecting the HEV target nucleic acid. The reactionmixture may further include a number of optional components such as, forexample, arrays of capture probe nucleic acids. For an amplificationreaction mixture, the reaction mixture will typically include otherreagents suitable for performing in vitro amplification such as, e.g.,buffers, salt solutions, appropriate nucleotide triphosphates (e.g.,dATP, dCTP, dGTP, dTTP, ATP, CTP, GTP and UTP), and/or enzymes (e.g.,reverse transcriptase, and/or RNA polymerase), and will typicallyinclude test sample components, in which an HEV target nucleic acid mayor may not be present. In addition, for a reaction mixture that includesa detection probe together with an amplification oligomer combination,selection of amplification oligomers and detection probe oligomers for areaction mixture are linked by a common target region (i.e., thereaction mixture will include a probe that binds to a sequenceamplifiable by an amplification oligomer combination of the reactionmixture).

Also provided by the subject invention are kits for practicing themethods as described herein. A kit in accordance with the presentinvention at least comprises one or more of the following: anamplification oligomer combination as described herein for amplificationof an HEV target nucleic acid; a capture probe oligomer as describedherein for purifying the HEV target nucleic acid; a detection probeoligomer as described herein for determining the presence or absence ofan HEV amplification product; and a probe protection oligomer asdescribed herein for detuning sensitivity of an assay for detecting theHEV target nucleic acid. The kits may further include a number ofoptional components such as, for example, arrays of capture probenucleic acids. Other reagents that may be present in the kits includereagents suitable for performing in vitro amplification such as, e.g.,buffers, salt solutions, appropriate nucleotide triphosphates (e.g.,dATP, dCTP, dGTP, dTTP, ATP, CTP, GTP and UTP), and/or enzymes (e.g.,reverse transcriptase, and/or RNA polymerase). Oligomers as describedherein may be packaged in a variety of different embodiments, and thoseskilled in the art will appreciate that the invention embraces manydifferent kit configurations. For example, a kit may includeamplification oligomers for only one target region of an HEV genome, orit may include amplification oligomers for multiple HEV target regions.In addition, for a kit that includes a detection probe together with anamplification oligomer combination, selection of amplification oligomersand detection probe oligomers for a kit are linked by a common targetregion (i.e., the kit will include a probe that binds to a sequenceamplifiable by an amplification oligomer combination of the kit). Incertain embodiments, the kit further includes a set of instructions forpracticing methods in accordance with the present invention, where theinstructions may be associated with a package insert and/or thepackaging of the kit or the components thereof.

The invention is further illustrated by the following non-limitingexamples.

Example 1

This example describes amplification reactions using various primer setsfor amplification of an HEV target region. Table 2 below lists all theamplification oligomers used in this assay.

TABLE 2 HEV Amplification Oligomers Class SEQ ID NO: nonT7 50 53 52 3130 29 66 65 64 62 35 34 33 61 T7 17 18 19 20  9 10 11 12 15 14

Each possible combination of the T7 and nonT7 primers listed in Table 2were tested. Primers were tested in a transcription-mediatedamplification (TMA) reaction using an HEV in vitro transcript (IVT) at15 and 0 copies/reaction. Transcription mediated amplification (TMA)reactions were carried out essentially as described by Kacian et al., inU.S. Pat. No. 5,399,491, the disclosure of this U.S. patent having beenincorporated by reference hereinabove. Amplification reactions wereconducted for various primer combinations using about 5 to 10 pmoles perreaction of each T7 primer and nonT7 primer. Amplification products weredetected by hybridization protection assay (HPA) using an AE-labeleddetection probe (having the nucleobase sequence shown in SEQ ID NO:67).Signal-to-noise ratios were calculated for each primer pair by dividingthe RLU value observed at 15 copies of HEV IVT by the background RLUvalue observed at 0 copies of HEV IVT. The results are shown in Table 3below.

TABLE 3 Signal-to-Noise Ratio of HEV T7/nonT7 Primer Pairs nonT7† 66 6564 62 61 53 52 50 35 34 33 31 30 29 T7†  9 898.1 896.5 487 802.2 599.21.6 0.9 75 916.5 361.1 956.7 910 943.3 1010 10 1183.7 974.4 1078.31023.6 1097.1 5.2 2.9 289.1 994.3 971.8 282.3 1102.3 22.9 907 11 1252.11286.2 933.6 1023 709.5 12 4 314.6 1013.3 1139.3 1044.1 308 14.9 906.312 944.6 980.1 1007.9 1061.4 595.1 675.9 26 1026.2 966.6 942.8 927.6945.7 953.4 854.5 14 3204.9 3120.2 2855.6 2919.1 2576.4 1001.5 1.6 891.92282.4 2574.2 2809.9 1800.1 227.1 679.9 15 1545.2 2074.8 2578.8 1361.22639.7 252.3 2.4 433.5 1253.3 2690.7 2161.8 313.7 1782.1 1058.6 17 273.8429.2 498 220.6 281.2 0.7 3.3 8.5 135.4 222.5 65.9 201.8 1.7 233.9 18914 445.7 896.2 906.3 780 0.9 0.9 1.1 809.1 716 171.2 1377.4 3 1191.2 19406.4 983.8 1135.8 750.1 703.8 1.1 1 1.6 981.4 836.6 496.4 1512.5 135.61075 20 1225.7 1048.4 898.3 752.8 786.5 124.9 1 345.5 886.1 892.5 737.51249.7 932.2 1197.9 †NonT7 primer designations are the SEQ ID NOs, aslisted in Table 2, supra. Similarly, T7 primer designations are the SEQID NOs, as listed in Table 2, supra.

Primer pairs that demonstrated a signal-to-background ratio of at least10 or more were considered to be successful for amplification of HEVtarget nucleic acid to at least as low as 15 copies per reaction, whilethose pairs demonstrating a ratio of below 10 were considered to beunsuccessful. Ratios over 10 are shown in bold in Table 3.

Example 2

This example describes HEV amplification and detection assays performedusing different oligomer combinations. Reagents, oligonucleotides, andsamples used in these experiments are listed in Tables 4-6 below.

TABLE 4 HEV Assay Reagents Reagent Name Description Internal Control AHEPES buffered solution containing Reagent detergent and an RNAtranscript. Target Capture A HEPES buffered solution containingdetergent, Reagent capture oligonucleotides and magnetic microparticles.Amplification Primers, dNTPs, NTPs and co-factors in TRIS bufferedReagent solution containing ProClin 300 as preservative. Enzyme MMLVReverse Transcriptase and T7 RNA Reagent Polymerase in HEPES/TRISbuffered solution containing 0.05% sodium azide as preservative. ProbeChemiluminescent oligonucleotide probes in succinate Reagent bufferedsolution containing detergent. HEV Negative A HEPES buffered solutioncontaining detergent. Calibrator HEV Positive A HEPES buffered solutioncontaining Calibrator detergent and an HEV RNA transcript.

TABLE 5 HEV-specific Oligonucleotides Class SEQ ID NO: Target Capture 74Oligo Target Capture 76 Oligo Target Capture 43 Oligo Target Capture  3Oligo Target Capture  7 Oligo Non-T7 Primer 29 Non-T7 Primer 66 Non-T7Primer 65 Non-T7 Primer 64 Non-T7 Primer 62 T7 Primer 12 T7 Primer 15 AELabeled 67 Probe AE Labeled 55 Probe AE Labeled 55 Probe AE Labeled 55Probe

TABLE 6 Samples Tested Sample Description Positive Sample HEV In VitroTranscript (IVT) in IC buffer Negative Sample HEV negative serum

Steps Performed Principles of the Procedure

The HEV assay involved three main steps, which take place in a singletube: sample preparation; HEV RNA target amplification byTranscription-Mediated Amplification (TMA); and detection of theamplification products (amplicon) by the Hybridization Protection Assay(HPA).

During sample preparation, RNA was isolated from specimens via the useof target capture. The specimen was treated with a detergent tosolubilize the viral particles, denature proteins and release viralgenomic RNA. Oligonucleotides (“capture oligonucleotides”) that arehomologous to highly conserved regions of HEV were hybridized to the HEVRNA target, if present, in the test specimen. The hybridized target wasthen captured onto magnetic microparticles that were separated from thespecimen in a magnetic field. Wash steps were utilized to removeextraneous components from the reaction tube. Magnetic separation andwash steps were performed with a target capture system.

Target amplification occurred via TMA, which is a transcription-basednucleic acid amplification method that utilizes two enzymes, MMLVreverse transcriptase and T7 RNA polymerase. The reverse transcriptasewas used to generate a DNA copy (containing a promoter sequence for T7RNA polymerase) of the target RNA sequence. The T7 RNA polymeraseproduces multiple copies of RNA amplicon from the DNA copy template. TheHEV assay utilized the TMA method to amplify regions of HEV RNA.

Detection was achieved by HPA using single-stranded nucleic acid probeswith chemiluminescent labels that are complementary to the amplicon. Thelabeled nucleic acid probes hybridize specifically to the amplicon. TheSelection Reagent differentiated between hybridized and unhybridizedprobes by inactivating the label on unhybridized probes. During thedetection step, the chemiluminescent signal produced by the hybridizedprobe was measured by a luminometer and was reported as Relative LightUnits (RLU).

Internal Control was added to each test specimen and assay calibratorvia the working Target Capture Reagent. The Internal Control (IC) in theHEV assay controlled for specimen processing, amplification anddetection steps. Internal Control signal was discriminated from the HEVsignal by the differential kinetics of light emission from probes withdifferent labels. Internal Control-specific amplicon was detected usinga probe with rapid emission of light (flasher signal). Amplicon specificto HEV was detected using probes with relatively slower kinetics oflight emission (glower signal). The Dual Kinetic Assay (DKA) is a methodused to differentiate between the signals from flasher and glowerlabels.

Order of Steps

Target Capture: Nucleic acids underwent specimen processing and targetcapture prior to amplification essentially according to the proceduresdisclosed in published International Patent Application No.PCT/US2000/18685, except that templates were captured using Hepatitis Evirus target capture oligonucleotides having the sequences given herein.Notably, capture oligonucleotides do not participate in theamplification or detection reactions of the assay. Virus-containingsamples were combined with a target capture reagent to facilitatenucleic acid release and hybridization to capture oligonucleotidesdisposed on magnetic beads. Incubation were performed to capture HEVnucleic acids from the sample. Following the incubation, the magneticbeads and any capture target nucleic acids were transferred to amagnetic wash station for 10-20 min. for a wash step. Captured targetnucleic acids were then assayed in an amplification reaction.

Transcription mediated amplification (TMA) reactions were carried outessentially as described in Example 1. Isolated target nucleic acidswere combined with primers in amplification reagent (Table 2) heated to60° C. for 10 minutes and then cooled to 42° C. to facilitate primerannealing. Enzyme reagent was then added to the mixtures and theamplification reactions were carried out, as will be familiar to thosehaving an ordinary level of skill in the art.

Detection: After a one hour incubation at 42° C., the amplificationreaction volumes were subjected to hybridization assays employing probesinternally labeled with a chemiluminescent compound using techniquesfamiliar to those having an ordinary level of skill in the art, and thenused in amounts equivalent to about 2 E+06 to about 6 E+06 RLU for eachprobe in the hybridization reaction. (See e.g., U.S. Pat. Nos. 5,585,481and 5,639,604, the disclosures of these patents are incorporated byreference). Hybridization reactions were followed by addition of analiquot of 0.15 M sodium tetraborate (pH 8.5), and 1% TRITON X-100(Union Carbide Corporation; Danbury, Conn.). These mixtures were firstincubated at 60° C. for 10 minutes to inactivate the chemiluminescentlabel linked to unhybridized probe, and cooled briefly to roomtemperature (i.e., 15-30° C.) prior to reading the hybridization signal.Chemiluminescence due to hybridized probe in each sample was assayedusing commercially available instrumentation (Gen-Probe Incorporated;San Diego, Calif.) configured for injection of 1 mM nitric acid and 0.1%(v/v) hydrogen peroxide, followed by injection of a solution containing1 N sodium hydroxide. Results for the chemiluminescent reactions weremeasured in relative light units (RLU). In this procedure, thesignal/noise value corresponded to the chemiluminescent signal (measuredin RLU) generated by label associated with specifically hybridized probedivided by a background signal measured in the absence of a targetnucleic acid.

Results and Discussion Experiment I—Combining Amplification Systems

The objective was to test pairs of T7 and non-T7, as well as someindividually, in order to confirm which of the different primercombinations exhibited better performance and which individual primersfunctionally performed the best. Target capture reactions were performedusing SEQ ID NO:76 as a target capture oligomer. Detection reactionswere performed using SEQ ID NO:67 as an AE-labeled detection probeoligomer. Amplification oligomer combinations are shown in Table 7,below. After determining SEQ ID NO:29+SEQ ID NO:65 and SEQ ID NO:12primers work best in previous experiments, much of this experimentfocused on these particular primers. Increasing the concentrations ofsome primers were also tested to evaluate performance and function inthe system. Panels at 20 copies/mL HEV IVT (8 replicates) and BI0052negative serum (2 replicates) were tested for each amplification system.

TABLE 7 Experimental Design for Experiment I Amp* Amp Non-T7 Primer T7Primer Systems (SEQ ID NO) (SEQ ID NO)  1 29 12  2 65 12  3 29 + 65 12 4 29 + 65 15  5 29 + 65 12 + 15  6 29 + 65 12 + 15  7 29 + 65 12 + 15 8 29 + 65 12 + 15  9 29 + 65 12 + 15 10 29 12 + 15 11 66 12 + 15 12 6512 + 15 13 64 12 + 15 14 62 12 + 15 15 65 15 16 65 15 17 65 15 *In allAmp Systems except for 6, 7, 8, 9, 16 & 17, the Non-T7 Primers and theT7 Primers were used at roughly the same concentrations to one another.In Amp Systems 6, 7, 8, 9, 16 & 17 the following primer members wereused at twice the concentration of the other primers in the reaction;65, 29, 12, 15, 65 and 15, respectively.

Table 8 shows a summary for Experiment I. When paired with SEQ ID NO:12,SEQ ID NO:65 performed better than SEQ ID NO:29, as shown in the highermean RLU and lower % CV values (Amp systems 1 and 2). When paired withSEQ ID NO:29+SEQ ID NO:65, SEQ ID NO:12 performed better than SEQ IDNO:15, as shown in the higher mean RLU and lower % CV values (Ampsystems 3 and 4). As seen with Amp system 5, adding SEQ ID NO:15improved RLU signal compared to Amp system 3. Keeping SEQ ID NO:29+SEQID NO:65 both at 5 pmol/reaction showed better RLU and % CV performance(Amp system 5) than increasing SEQ ID NO:65 to 10 pmol/reaction in Ampsystem 6. When comparing Amp systems 8 and 9, increasing SEQ ID NO:12from 5 to 10 pmol/reaction showed better performance than increasing SEQID NO:15. Amp systems 10 through 14 compared which non-T7 would performwith higher RLUs and low % CVs. Based on the criteria, SEQ ID NO:66 andSEQ ID NO:64 showed the highest RLUs and lowest % CVs. Amp systems 15through 17 increased the concentration from 5 to 10 pmol/reaction ofeither the non-T7 or T7 in the system. Comparing Amp systems 15 and 16these data show that increasing SEQ ID NO:65 improved performance (Ampsystem 16) while, on the other hand, increasing SEQ ID NO:15 decreasedperformance (Amp system 17).

TABLE 8 Summary of Results for Experiment I RLU RLU RLU System PanelMean SD % CV S/CO % R Amp 1 20 c/mL 1,035,254 60,059 5.80 105.76 100 Amp2 20 c/mL 1,367,829 17,738 1.30 139.73 100 Amp 3 20 c/mL 1,265,44340,365 3.19 129.27 100 Amp 4 20 c/mL 354,741 412,106 116.17 36.24 100Amp 5 20 c/mL 1,307,112 39,148 2.99 133.53 100 Amp 6 20 c/mL 1,138,545346,932 30.47 116.31 100 Amp 7 20 c/mL 1,157,461 23,540 2.03 118.24 100Amp 8 20 c/mL 1,315,063 11,663 0.89 134.34 100 Amp 9 20 c/mL 993,828353,189 35.54 101.53 100 Amp 10 20 c/mL 1,110,792 102,117 9.19 113.47100 Amp 11 20 c/mL 1,377,343 45,052 3.27 140.70 100 Amp 12 20 c/mL1,343,435 66,431 4.94 137.24 100 Amp 13 20 c/mL 1,372,134 48,909 3.56140.17 100 Amp 14 20 c/mL 1,342,071 92,993 6.93 137.10 100 Amp 15 20c/mL 606,324 424,338 69.99 61.94 100 Amp 16 20 c/mL 1,089,242 259,10623.79 111.27 100 Amp 17 20 c/mL 395,478 164,783 41.67 40.40 100 RLU =Relative Light Units; SD = Standard Deviation; CV = Coefficient ofVariation; S/CO = Signal to Cutoff Ratio; % R = % Reactivity.

Experiment II—Confirming the Best Performing Primer Pair Combination

The objective was to test pairs of T7 and non-T7 and different primercombinations in the amplification reagent. Panel at 20 c/mL HEV IVT wastested in 5 replicates for each amplification system.

Table 9 shows the experimental design. All conditions stayed the sameexcept for the amplification systems tested. Target capture wasperformed using SEQ ID NO:76 and detection was performed using anAE-labeled SEQ ID NO:67 as a detection probe. As shown in Experiment I,Amp system 1 showed good performance, and that was set as a control. Ampsystems 2 through 4 tested how each non-T7 compared to each other whenonly paired with SEQ ID NO:15. Since SEQ ID NO:66, SEQ ID NO:64, and SEQID NO:62 showed good RLU and % CV performance in Experiment I, eachthese non-T7s were tested in the primer pairing combinations shown inAmp systems 5 through 7.

TABLE 9 Experimental Design for Experiment II Amp* Amp Non-T7 T7 Systems(SEQ ID NO) (SEQ ID NO) 1 29 + 65 12 + 15 2 66 15 3 64 15 4 62 15 5 29 +66 12 + 15 6 29 + 64 12 + 15 7 29 + 62 12 + 15

Table 10 shows a summary for Experiment II. When comparing Amp systems 2through 4, SEQ ID NO:64 showed best performance in higher mean RLUcompared to SEQ ID NO:66 and SEQ ID NO:62. When comparing Amp systems 1and 6, SEQ ID NO:29 paired with SEQ ID NO:64 performed better than SEQID NO:29+SEQ ID NO:65. Even though Amp system 5 showed the highest RLUperformance when compared with Amp systems 6 and 7, Amp system 6 waschosen for further study based on sequence alignment.

TABLE 10 Summary of Results for Experiment II RLU System Panel RLU MeanRLU SD % CV S/CO % R Amp 1 20 c/mL 1,054,954 455,280 43.16 107.77 100Amp 2 20 c/mL 108,457 79,457 73.26  11.08 100 Amp 3 20 c/mL 386,281308,958 79.98  39.46 100 Amp 4 20 c/mL 166,652 96,680 58.01  17.02 100Amp 5 20 c/mL 1,251,195 73,533 5.88 127.82 100 Amp 6 20 c/mL 1,219,780130,591 10.71 124.61 100 Amp 7 20 c/mL 1,242,616 54,910 4.42 126.94 100RLU = Relative Light Units; SD = Standard Deviation; CV = Coefficient ofVariation; S/CO = Signal to Cutoff Ratio; % R = % Reactivity.

Experiment III—Screening New Probe Pairs

The objective was to test new probe oligo pairs and evaluate theperformance. Each of the probes was also tested individually to evaluateperformance. Panel at 0 (IC buffer only) and 1,000 copies/mL HEV IVTwere tested as negative and positive calibrators, respectively, of theassay. Panel at 20 copies/mL of HEV IVT and BI0052 negative serum weretested as samples at 7 replicates each. Each panel type was tested foreach probe condition.

Table 11 shows the experimental design. All conditions stayed the sameexcept for the 7 probe systems tested. Internal control (IC) probe wasalso added to each of the 7 probes listed in the table.

TABLE 11 Experiments Design for Experiment III Probe Probe # Probe^(‡)(RLU/rxn) TCOs in TCR Primers in Amp* Probe 1 SEQ ID NO: 67 2.00E+06 SEQID NO: 43 SEQ ID NO: 29 SEQ ID NO: 12 Probe 2 SEQ ID NO: 55 [8, 9]3.00E+06 SEQ ID NO: 3  + + Probe 3 SEQ ID NO: 55 [10, 11] 3.00E+06 SEQID NO: 7  SEQ ID NO: 64 SEQ ID NO: 15 Probe 4 SEQ ID NO: 55 [12, 13]6.00E+06 Probe 5 SEQ ID NO: 67 2.00E+06 SEQ ID NO: 55 [12, 13] 6.00E+06Probe 6 SEQ ID NO: 55 [8, 9] 3.00E+06 SEQ ID NO: 55 [12, 13] 6.00E+06Probe 7 SEQ ID NO: 55 [10, 18] 3.00E+06 SEQ ID NO: 55 [12, 13] 6.00E+06IC Probe SEQ ID NO: 78- 1.00E+06 added to PPO Hybrid Probes #1-7 ^(‡)The[#, #] designation refers to the nucleobase residues (counting from 5′to 3′) between which a chemiluminescent label was located for SEQ ID NO:55. *SEQ ID NO: 64 was tested at 2 × the concentration per reactioncompared to each of SEQ ID NOs: 12, 15 & 29.

Table 12 shows a summary for Experiment III. When looking at the probereagents containing probe pairs (Probes 5, 6, and 7), probes 5 and 6showed low background (low analyte RLU in the Negative Calibrator andBI0052 negative serum), and high analyte RLU signal in the PositiveCalibrator and HEV IVT at 20 c/mL. Probe 7 also showed a similar result.Of the three probes (Probes 5, 6, and 7), Probe 5 had the highestanalyte RLU signal in the positive samples. For the individual probeperformance (Probes 1 through 4), SEQ ID NO:67 showed the highestanalyte RLU signal in the positive samples, which relatively highbackground signal in the negative samples.

TABLE 12 Summary of Results for Experiment III-IC RLU and analyte RLU ICRLU Analyte RLU 95% 95% Condition Panel Mean SD % CV CI Mean SD % CV CIProbe1 Neg Cal 134,234 6,423 4.78 454 468 103.06 Probe1 Pos Cal 1k134,264 22,989 17 1,207,525 10,587 0.88 c/mL Probe1 20 c/mL HEV 134,66725,652 19.05 19,003 1,129,086 121,191 10.73 89,778 IVT Probe1 BI0052 BN140,531 12,824 9.13 9,500 626 756 120.61 560 593600 Probe2 Neg Cal130,780 3,363 2.57 595 217 36.46 Probe2 Pos Cal 1k 130,740 12,322 91,209,761 16,267 1.34 c/mL Probe2 20 c/mL HEV 178,999 26,435 14.7719,583 855,109 371,340 43.43 275,087 IVT Probe2 BI0052 BN 126,281 9,8607.81 7,304 916 265 28.93 196 593600 Probe3 Neg Cal 134,046 4,495 3.35144 250 173.21 Probe3 Pos Cal 1k 134,061 9,411 7 854,435 10,650 1.25c/mL Probe3 20 c/mL HEV 132,559 18,420 13.90 13,645 649,395 287,95444.34 213,316 IVT Probe3 BI0052 BN 134,791 9,170 6.80 6,793 432 609140.93 451 593600 Probe4 Neg Cal 127,697 7,878 6.17 4,580 376 8.21Probe4 Pos Cal 1k 127,584 1,216 1 379,813 8,359 2.20 c/mL Probe4 20 c/mLHEV 135,488 2,617 1.93 1,939 160,017 74,978 46.86 55,543 IVT Probe4BI0052 BN 129,564 5,516 4.26 4,086 4,189 461 11.01 342 593600 Probe5 NegCal 135,336 2,380 1.76 5,778 1,312 22.70 Probe5 Pos Cal 1k 135,756 5,5614 1,585,647 9,575 0.60 c/mL Probe5 20 c/mL HEV 136,693 9,838 7.20 7,2881,131,831 490,936 43.38 363,684 IVT Probe5 BI0052 BN 129,554 10,328 7.977,651 6,440 1,997 31.01 1,479 593600 Probe6 Neg Cal 135,671 4,178 3.086,024 488 8.11 Probe6 Pos Cal 1k 135,139 8,626 6 1,468,351 32,266 2.20c/mL Probe6 20 c/mL HEV 169,229 32,044 18.94 23,738 787,965 610,39977.47 452,181 IVT Probe6 BI0052 BN 141,381 6,476 4.58 4,797 5,965 90115.11 668 593600 Probe7 Neg Cal 131,353 1,086 0.83 6,194 415 6.71 Probe7Pos Cal 1k 131,669 15,624 12 1,200,190 17,730 1.48 c/mL Probe7 20 c/mLHEV 189,382 12,230 6.46 9,060 1,062,012 44,717 4.21 33,126 IVT Probe7BI0052 BN 139,499 9,591 6.88 7,105 5,746 694 12.09 514 593600 RLU =Relative Light Units; SD = Standard Deviation; CV = Coefficient ofVariation; CI = Confidence Interval

Table 13 shows a summary of the mean analyte S/CO values, including thereactivity, and validity, for Experiment III.

TABLE 13 Summary of Results for Experiment III-Analyte S/CO, Reactivity,and Validity Analyte S/CO Condition Panel Mean SD % CV 95% CI NR RInvalid Valid % R Probe1 Neg Cal 0.01 0.01 103.06 0 Probe1 Pos Cal lkc/mL 32.92 0.29 0.88 0 Probe1 20 c/mL HEV 30.78 3.30 10.73 2.45 0 7 0 7100 IVT Probe1 BI0052 BN 0.02 0.02 120.61 0.02 7 0 0 7 0 593600 Probe2Neg Cal 0.02 0.01 36.46 0 Probe2 Pos Cal lk c/mL 32.80 0.44 1.34 0Probe2 20 c/mL HEV 23.18 10.07 43.43 7.46 1 6 0 7 86 IVT Probe2 BI0052BN 0.02 0.01 28.93 0.01 7 0 0 7 0 593600 Probe3 Neg Cal 0.01 0.01 173.210 Probe3 Pos Cal lk c/mL 33.15 0.41 1.25 0 Probe3 20 c/mL HEV 25.1911.17 44.34 8.28 1 6 0 7 86 IVT Probe3 BI0052 BN 0.02 0.02 140.93 0.02 70 0 7 0 593600 Probe4 Neg Cal 1.00 0.08 8.21 3 Probe4 Pos Cal lk c/mL82.93 1.83 2.20 3 Probe4 20 c/mL HEV 34.94 16.37 46.86 12.13 0 0 7 0#DIV/0! IVT Probe4 BI0052 BN 0.91 0.10 11.01 0.07 0 0 7 0 #DIV/0! 593600Probe5 Neg Cal 0.11 0.02 22.70 0 Probe5 Pos Cal lk c/mL 29.72 0.18 0.600 Probe5 20 c/mL HEV 21.22 9.20 43.38 6.82 0 7 0 7 100 IVT Probe5 BI0052BN 0.12 0.04 31.01 0.03 7 0 0 7 0 593600 Probe6 Neg Cal 0.12 0.01 8.11 0Probe6 Pos Cal lk c/mL 29.32 0.64 2.20 0 Probe6 20 c/mL HEV 15.74 12.1977.47 9.03 1 6 0 7 86 IVT Probe6 BI0052 BN 0.12 0.02 15.11 0.01 7 0 0 70 593600 Probe7 Neg Cal 0.15 0.01 6.71 0 Probe7 Pos Cal lk c/mL 28.440.42 1.48 0 Probe7 20 c/mL HEV 25.17 1.06 4.21 0.78 0 7 0 7 100 IVTProbe7 BI0052 BN 0.14 0.02 12.09 0.01 7 0 0 7 0 593600 S/CO = Signal tocutoff ratio; SD = Standard Deviation; CV = Coefficient of Variation; CI= Confidence Interval; NR = Non-Reactive; R = Reactive; % R = %Reactivity

Example 3

This example describes evaluation of analytical sensitivity,cross-reactivity, specificity, and further probe formulation for an HEVamplification and detection assay. Reagents are as previously describedin Example 2. Oligonucleotides and samples used in these experiments arelisted in Tables 14 and 15 below.

TABLE 14 HEV-specific Oligonucleotides and InternalControl Flasher Probe and PPO SEQ ID NO Class¹ Sequence (5′-3′) 64Non-T7 TGCTGCCCGCGCCAC Primers 29 Non-T7 CCGGCGGTGGTTTCT Primers 37AE Labeled gaccggguugauucuC Probes 67 AE Labeled ugauucucagcccuucgCProbes 71 AE Labeled ugauugucagcccuucgC Probes 36 Probe GAAGGGCTGAGAATCAProtection Oligos 40 Probe GAGAATCAACCCGGT Protection Oligos 12T7 Promoter AATTTAATACGACTCACTATAGGGAG PrimersAAGGGGTTGGTTGGATGAATATAGGG GA 15 T7 Promoter AATTTAATACGACTCACTATAGGGAGPrimers AGGGCGAAGGGGTTGGTTGGATGAA 3 Capture aagacauguuauucauuccacccTTTAAOligos AAAAAAAAAAAAAAAAAAAAAAAAAAAA 7 CaptureaagacauguuauucauucuacccTTTAA Oligos AAAAAAAAAAAAAAAAAAAAAAAAAAAA 43Capture gaggggcgcugggacuggucgTTTAAAA Oligos AAAAAAAAAAAAAAAAAAAAAAAAAA78 AE Labeled ccacaagcuuagaagauagagagG Probes 79 Probe CTATCTTCTAAGCTTGProtection Oligos ¹Lower case = methoxy RNA; Upper case = DNA

TABLE 15 Samples Tested Sample Description Source Matrix HEV Standard1st World Health Organization PEI (Paul Ehrlich Lyophilized (6329/10)International Standard for Hepatitis E Institute) plasma Virus RNANucleic Acid Amplification Techniques (NAT)-Based Assays HEV RNA HEVgenotypes 1-4 In-house IC buffer transcripts HEV negative Frozen plasma,2100 unique donors BocaBiolistics plasma plasma

Steps Performed

Assay steps were performed as described in Example 2.

Results and Discussion Analytical Sensitivity

Analytical sensitivity of the HEV assay on was determined using the 1stWorld Health Organization (WHO) International Standard (IS) for HEV RNANucleic Acid Amplification Techniques (NAT)-Based Assays (PEI code6329/10). The WHO IS is based on HEV genotype 3a derived from a clinicalisolate (GenBank accession number AB630970) first obtained by the PaulEhrlich Institute (Langen, Germany) from the Hokkaido Red Cross [part ofThe Japanese Red Cross (JRC)].

The sensitivity was determined to be 8.4 International Unit (IU)/mL at95% detection level for HEV WHO IS.

TABLE 16 Analytical Sensitivity with the WHO Standard for HEV PercentInternational Reactivity Units/mL of HEV (n = 81) WHO IS 90 100 30 10010  91  3  52  1  22  0  0 Detection Probability Limit of Detection byProbit Analysis* in IU/mL 95% LOD 8.4 (6.3-12.8) (95% fiducial limits)50% LOD 1.7 (1.4-2.1) (95% fiducial limits) *Using SAS 9.2 Probit normalmodel

Analytical sensitivity of HEV Assay among various HEV genotype IVTs. RNAIVTs were prepared for each of the major known HEV genotypes 1-4,including three sub-genotypes for HEV-3, namely HEV-3a, HEV-3b andHEV-3f. HEV-3a IVT is used as the HEV assay Positive Calibrator. Inaddition, RNA IVT was also made for a putative HEV genotype 6. Thesensitivity for each of the major HEV genotype/subgenotype IVT wasdetermined to be in the range of 10-19 c/mL at 95% detection level. Theexception is with the putative HEV genotype 6 in which the sensitivityof the HEV Assay is about 5 times lower compared to the averagesensitivity of HEV genotype 1-4 IVTs. The lower detection of theputative HEV genotype 6 strain in the HEV assay is mitigated by the factthat there is only one strain (wbJOY_06; GenBank accession numberAB602441) associated with the putative genotype 6, that it was found ina single wild boar in Japan, and that it has not been associated withany known human HEV cases (Takahashi M et al., J. Gen. Virol.92:902-908, 2011).

TABLE 17 Analytical Sensitivity among HEV Genotype IVTs Copies/mLPercent Reactivity of Genotype^(a) IVTs (n = 81) 1 2 3a 3b 3f 4c 6^(b)90 100 100 100 100 100 100 98 30 100 100 100 99 100 98 88 10 94 94 91 9495 90 46 3 44 49 52 42 60 42 16 1 17 25 22 17 21 21 7 0 0 0 0 0 0 0 0Detection Probability by Probit Analysis^(c) Limit of Detection (LOD) inCopies/mL 95% LOD 12.7 13.0 13.7 14.6 10.2 18.9 69.6 (95% fiducial (9.6-18.6)  (9.6-19.7) (10.1-20.7)   (11-21.5)  (7.7-15.2) (13.9-28.8)(35.3-256.7) limits) 50% LOD  2.8  2.4  2.5  2.9  2.2  2.9  9.0 (95%fiducial (2.4-3.3) (2.0-2.9) (2.0-3.0) (2.4-3.5) (1.8-2.6) (2.4-3.6)(5.5-14.8) limits) ^(a)Based on GenBank accession numbers NC001434 (1),M74506 (2), AB630970 (3a), AB630971 (3b), FJ956757 (3f), AB161717 (4c)and AB602441 (6) ^(b)Putative HEV genotype ^(c)Using SAS 9.2 PROBITnormal model

Cross-Reactivity

In silico BLAST analysis of the HEV-specific oligos did not showsequence matches to other blood borne pathogens except hepatitis C virus(HCV). The HEV oligo SEQ ID NO:64 showed 100% identity to part of theHCV envelope gene (positions 199-213 in GenBank accession numberJQ063881). It is expected that this will not cause any false positivityissue because all the rest of the HEV-specific oligo sequences (whole orin part) are not found in the HCV genomic sequence. This is supported bytesting of HCV-positive samples which showed non-reactivity in the HEVassay. Other bloodborne viruses (human immunodeficiency virus 1,hepatitis B virus, and West Nile virus) tested were also non-reactivefor the HEV assay.

TABLE 18 HEV Cross-reactivity with Bloodborne Pathogens Blood Borne Mean% Condition Viruses Added Level n S/CO* Reactivity HEV Positive HIV-1Type B (IIIB)   100 c/mL 8 23.57 100% (30 IU/mL HIV-1 Group O   100 c/mL9 27.95 100% WHO IS HCV 1A   100 c/mL 9 28.34 100% added) HCV 2B  ~300c/mL 9 28.32 100% HBV ~32 IU/mL 8 25.84 100% WNV Sample 022 3,000 c/mL 928.74 100% WNV Sample 688 3,000 c/mL 9 28.15 100% WNV Sample 630 3,000c/mL 9 22.64 100% HEV HIV-1 Type B (IIIB)   100 c/mL 9  0.01  0%Negative HIV-1 Group O   100 c/mL 9  0.02  0% HCV 1A   100 c/mL 9  0.02 0% HCV 2B  ~300 c/mL 8  0.03  0% HBV ~32 IU/mL 9  0.02  0% WNV Sample022 3,000 c/mL 9  0.01  0% WNV Sample 688 3,000 c/mL 9  0.03  0% WNVSample 630 3,000 c/mL 9  0.02  0% *S/CO (Signal to Cutoff) > or = 1.0considered reactive

Specificity

The specificity of the HEV assay on was determined to be 99.95% (95%Score CI: 99.73%-99.99%) for 2,100 unlinked, frozen plasma specimens.The data showed excellent specificity of the HEV assay in frozen plasmaspecimens.

TABLE 19 HEV Specificity on Frozen Plasma Specimens N % Specimens Tested2,100 100 Valid Results 2,100 100 Initial Reactive 1 0.05 RepeatReactive 0 0 Specificity (95% CI)* 99.95% (99.73-99.99) *CI = ConfidenceInterval using Score method

Probe Design

HEV probe oligo SEQ ID NO:71 showed an increased detection signal forHEV-3f relative to SEQ ID NO:55 [12,13], increasing the HEV 3fsensitivity from an 95% LOD of 12.4 c/mL to 10.2 c/mL and the RLU signalto a level more comparable to the other HEV genotypes tested.

Example 4

This example describes the determination of HEV RNA prevalence in blooddonors and the performance characteristics of an HEV amplification anddetection assay using oligonucleotides as described above.

Methods

Studies were conducted to show the analytical sensitivity to the HEV WHOInternational Standard (Paul Ehrlich Institute (PEI) code 6329/10) andRNA transcripts of all four clinically relevant HEV genotypes (1-4), andclinical specificity of the HEV assay described above (“the HEV assay”).Plasma (for nucleic acid testing) was collected from ˜10,000 unlinked,volunteer whole blood donors. Samples were tested for HEV RNA using theHEV assay on the automated Panther system (Hologic, Inc., cat. no.303095). Samples that were repeatedly reactive using TMA were confirmedby PCR and sequence analysis.

Results

The HEV assay showed a 95% limit of detection (LOD) of 7.9 IU/mL usingthe WHO Standard and 14.4 copies/mL using HEV 3a RNA transcript that hadthe same sequence as the HEV WHO Standard (see Tables 20 and 21). Theassay detected all four HEV genotypes with a 95% LOD ranging from 7.9 to17.7 copies/mL using RNA transcripts for HEV 1, 2, 3a, 3b, 3f and 4c(see Table 23). A total of 9,998 blood donations were screened for HEVRNA using the TMA assay. Three TMA repeat reactive donations wereidentified and confirmed positive by testing independent aliquots withPCR. One sample was determined to be genotype 3f by sequence analysis.Based on this study, HEV RNA prevalence rate in these blood donationswas estimated to be 1 in 3,333 or 0.03% and the clinical specificity ofthe HEV assay was determined to be 99.99% (see Table 22 and Table 24).

TABLE 20 Analytical Sensitivity to HEV WHO International Standard (PEI)code 6329/10 % Reactivity (95% CI) 90^(†) 30 10 3 1 0 HEV WHO 100 100 9867 27 0 IU/mL (98-100) (98-100) (94-99) (60-74) (20-34) (0-5) (95% CI)HEV3a IVT 100 100 88 38 20 0 c/mL (95-100) (95-100) (71-93) (28-49)(14-31) (0-5) (95% CI) WHO, n = 162, In Vitro Transcript (IVT) &negative n = 81 ^(†)The values 90, 30, 10, 3, 1 and 0 in the row abovethe percent reactivity results refer to IU/mL in the TMA reaction forthe HEV WHO standard, and refer to copies/mL in the TMA reaction for theHEV3a IVT.

TABLE 21 Analytical Sensitivity to HEV WHO International Standard (PEI)code 6329/10 Detection HEV WHO Std IU/mL HEV3a IVT, c/mL Probability(95% Fiducial Limits) (95% Fiducial Limits) 95% 7.89 (6.63-9.83) 14.40(11.28-20.14) 50% 2.02 (1.71-2.32) 3.63 (2.92-4.37) 

TABLE 22 HEV RNA Prevalence Among Blood Donations n HEV RNA Prevalence(Rate) 9,998 3 or 1 in 3,333 (0.03%; 95% CI: 0.01%-0.09%)

TABLE 23 Analytical Sensitivity to HEV Genotype 1-4 In Vitro TranscriptsCopies/mL Percent Reactivity of Genotype¹ IVTs (n = 81) HEV1 HEV2 HEV3aHEV3b HEV3f HEV4c 90 100 100 100 100 100 100 30 100 100 100 100 100 10010 96 95 88 86 98 80 3 77 42 38 46 59 36 1 31 27 20 12 20 19 0 0 0 0 0 00 Detection Probability² Limit of Detection in Copies/mL 95% LOD 7.8811.32 14.40 13.72 8.26 17.66 (95% fiducial limits)  6.11-11.26 8.83-16.03 11.28- 10.89-  6.65-11.11 13.77-24.74 20.14 18.78 50% LOD1.64  2.84  3.63  3.74 2.48  4.16 (95% fiducial limits) 1.21-2.062.26-3.44 2.92-4.37 3.03-4.47 2.01-2.96 3.34-5.03 ¹Based on GenBankaccession numbers NC001434 (1), M74506 (2), AB630970 (3a), AB630971(3b), FJ956757 (3f), AB161717 (4c) ²SAS Enterprise Guide 5.1 ProbitAnalysis using Gompertz model

TABLE 24 HEV Assay Specificity Testing Results of Blood Donations n %#Unique Donations Tested 9,998 100.00  #Valid Nonreactive Retest Results9,995 99.97 #Initial Reactives 4  0.04 #Repeat Reactives 3  0.03Specificity Rate 99.99% (95% CI: 99.94%-100.00%)

Discussion/Conclusion

Results showed that the HEV assay was sensitive and specific, anddetected all four clinically relevant HEV genotypes. Testing of nearly10,000 individual blood donors for this study yielded three HEV RNAconfirmed positive donations resulting in an HEV RNA prevalence rate of0.03%. Based on the performance demonstrated in this study, the HEVassay may be useful for screening blood donations for HEV RNA.

Sequences

TABLE 25 Exemplary Oligomer Sequences, Reference Sequences, and RegionsSEQ ID NO: Oligonucleotide Sequence Oligonucleotide Description  1Accession No. AB074918.2 GI: 21218075 HEV reference sequence  2aagacauguuauucauuccaccc Target-hybridizing sequence of SEQ ID NO: 2  3aagacauguuauucauuccacccTTTAAAAA Target capture oligoAAAAAAAAAAAAAAAAAAAAAAAAA  4 aagacauguuauucauucYWcccTarget-hybridizing sequence of target capture oligo  5TgaTTgTcagcccTTcgC Probe  6 aagacauguuauucauucuacccTarget-hybridizing sequence of SEQ ID NO: 7  7aagacauguuauucauucuacccTTTAAAAA Target capture oligo  AAAAAAAAAAAAAAAAAAAAAAAAA  8 aagacauguuauucauucYWcccTTTAAAAATarget capture oligo AAAAAAAAAAAAAAAAAAAAAAAAA  9AATTTAATACGACTCACTATAGGGAGAAGGG T7 amp oligo GTTGGTTGGATGAATATAG 10AATTTAATACGACTCACTATAGGGAGAAGGG T7 amp oligo GTTGGTTGGATGAATATAGG 11AATTTAATACGACTCACTATAGGGAGAAGGG T7 amp oligo GTTGGTTGGATGAATATAGGG 12AATTTAATACGACTCACTATAGGGAGAAGGG T7 amp oligo GTTGGTTGGATGAATATAGGGGA 13ctatgctgcccgcgccaccg Amp oligo hybridizing region 14AATTTAATACGACTCACTATAGGGAGAGGCG T7 amp oligo AAGGGGTTGGTTGGATGAA 15AATTTAATACGACTCACTATAGGGAGAGGGC T7 amp oligo GAAGGGGTTGGTTGGATGAA 16ccggcggtggtttctggggtgac Amp oligo hybridizing region 17AATTTAATACGACTCACTATAGGGAGAGGTT T7 amp oligo GGTTGGATGAATATAG 18AATTTAATACGACTCACTATAGGGAGAGGTT T7 amp oligo GGTTGGATGAATATAGG 19AATTTAATACGACTCACTATAGGGAGAGGTT T7 amp oligo GGTTGGATGAATATAGGG 20AATTTAATACGACTCACTATAGGGAGAGGTT T7 amp oligo GGTTGGATGAATATAGGGGA 21AGGGGTTGGTTGGATGAATATAG Target-hybridizing sequence of SEQ ID NO: 9 22AGGGGTTGGTTGGATGAATATAGG Target-hybridizing sequence of SEQ ID NO: 10 23AGGGGTTGGTTGGATGAATATAGGG Target-hybridizing sequence of SEQ ID NO: 1124 AGGGGTTGGTTGGATGAATATAGGGGATarget-hybridizing sequence of SEQ ID NO: 12 25 GGTTGGTTGGATGAAAmp oligo core sequence 26 tgctgcccgcgcc Amp oligo core sequence 27CGGCGGTGGTTTCT Amp oligo core sequence  28¹ NCGGCGGTGGTTTCTNNNon-T7 amp oligo 29 CCGGCGGTGGTTTCT Non-T7 amp oligo 30 CCGGCGGTGGTTTCTGNon-T7 amp oligo 31 CCGGCGGTGGTTTCTGG Non-T7 amp oligo 32CGGCGGTGGTTTCTGG Non-T7 amp oligo 33 CTATGCTGCCCGCGCC Non-T7 amp oligo34 CTATGCTGCCCGCGCCA Non-T7 amp oligo 35 CTATGCTGCCCGCGCCACNon-T7 amp oligo 36 GAAGGGCTGAGAATCA Probe protection oligo 37gaccggguugauucuC Probe 38 gaccggguugauucu Probe 39gacagggttgattctcagcccttcgccc Probe target region 40 GAGAATCAACCCGGTProbe protection oligo 41 gaccgggTTgaTTcTC Probe 42gaggggcgcugggacuggucg Target-hybridizing sequence of SEQ ID NO:43 43gaggggcgcugggacuggucgTTTAAAAAAA Target capture oligoAAAAAAAAAAAAAAAAAAAAAAA 44 tgcctatgctgcccgcgccaccggccggtcaAmp oligo hybridizing region gccgtctggccgtcgccgtgggcggcgcagcggcggtgccggcggtggtttctggggtgac 45 GGCGAAGGGGTTGGTTGGATGAATarget-hybridizing sequence of SEQ ID NO: 14 46 GGGCGAAGGGGTTGGTTGGATGAATarget-hybridizing sequence of SEQ ID NO: 15 47SGGCGAAGGGGTTGGTTGGATGAATATAGGG Amp oligo hybridizing region GA 48GGTTGGTTGGATGAATATAG Target-hybridizing sequence of SEQ ID NO: 17 49GGTTGGTTGGATGAATATAGG Target-hybridizing sequence of SEQ ID NO: 18 50GGTTGGTTGGATGAATATAGGG Target-hybridizing sequence of SEQ ID NO: 19 51GGTTGGTTGGATGAATATAGGGGA Target-hybridizing sequence of SEQ ID NO: 20 52GGTTTCTGGGGTGAC Non-T7 amp oligo 53 GTGGTTTCTGGGGTGA Non-T7 amp oligo 54GTGGTTTCTGGGGTGAC Non-T7 amp oligo 55 GUUGAUUCUCAGCCCUUCGCCC Probe 56SGGCGAAGGGGTTGGTTGGATGAA Target-hybridizing sequence of SEQ ID NO: 57 57AATTTAATACGACTCACTATAGGGAGAsGGC T7 amp oligo GAAGGGGTTGGTTGGATGAA 58acagggttgattctcagcccttcgccctccc Partial ampliconctatattcatccaaccaaccccttcgccs 59 ccggcggtggtttctggggtgacagggttgaPartial amplicon ttctcagcccttcgccc 60 tatgctgcccgcgccaccggccggtcagccgPartial amplicon tctggccgtcgccgtgggcggcgcagcggcggtgccggcggtggtttctggggtgacagggt tgattct 61 TGCCTATGCTGCCCGCGCCACNon-T7 amp oligo 62 TGCTGCCCGCGCCA Non-T7 amp oligo 63tgcctatgctgcccgcgccaccg Amp oligo hybridizing region 64 TGCTGCCCGCGCCACNon-T7 amp oligo 65 TGCTGCCCGCGCCACC Non-T7 amp oligo 66TGCTGCCCGCGCCACCG Non-T7 amp oligo 67 ugauucucagcccuucgC Probe 68agggttgattctcagcccttcgccc Probe target region 69gccggtcagccgtctggccgtcgccgtgggc Probe target regionggcgcagcggcggtgccggcggtggtttctg gggtgacagggttgattctcagcccttcgcc c 70tgcctatgctgcccgcgccaccggccggtca Amplicon gccgtctggccgtcgccgtgggcggcgcagcggcggtgccggcggtggtttctggggtgaca gggttgattctcagcccttcgccctcccctatattcatccaaccaaccccttcgccg 71 ugauugucagcccuucgC Probe 72ugauugucagcccuucg Probe 73 AATTTAATACGACTCACTATAGGGAGAT7 promoter sequence 74 accgccgcugcgccgcccacggcgTTTAAAATarget capture oligo AAAAAAAAAAAAAAAAAAAAAAAAAA 75accgccgcugcgccgcccacggcg Target-hybridizing sequence of SEQ ID NO: 74 76agcggcggggcgcugggccuggucTTTAAAA Target capture oligoAAAAAAAAAAAAAAAAAAAAAAAAAA 77 agcggcggggcgcugggccuggucTarget-hybridizing sequence of SEQ ID NO: 76 78 ccacaagcuuagaagauagagagGInternal control probe 79 CTATCTTCTAAGCTTG Probe protection oligo Notethat the amplicon and partial amplicon sequences are illustrated hereinand in the Sequence Listing as DNA, however, ordinarily skilled artisansunderstand that amplification products generated during TMA reactionsare either RNA or DNA, depending upon the stage in the amplificationcycle. DNA designation is provided herein only for convenience, and notlimitation. ¹N at position 1 is C or is absent, N at position 16 is G oris absent, and N at position 17 is G or is absent. In some embodiments,if N at position 16 is G and N at position 17 is absent, then N atposition 1 is C.

From the foregoing, it will be appreciated that, although specificembodiments of the invention have been described herein for purposes ofillustration, various modifications may be made without deviating fromthe spirit and scope of the invention. Accordingly, the invention is notlimited except as by the appended claims. All publications, patents, andpatent applications cited herein are hereby incorporated by reference intheir entireties for all purposes.

What is claimed is:
 1. A kit for determining the presence or absence ofhepatitis E virus (HEV) in a sample, the kit comprising: (1) anamplification reagent comprising at least two amplification oligomersfor amplifying a target region of an HEV target nucleic acid, wherein(a) at least one amplification oligomer is selected from the groupconsisting of (i) an oligomer comprising a target-hybridizing sequenceconsisting of a sequence that is from about 14 to about 23 contiguousnucleotides contained in the sequence of SEQ ID NO:63 and that includesat least the sequence of SEQ ID NO:26, including RNA equivalents andDNA/RNA chimerics thereof, and (ii) an oligomer comprising atarget-hybridizing sequence consisting of SEQ ID NO:28, including RNAequivalents and DNA/RNA chimerics thereof; and (b) at least oneamplification oligomer is a promoter primer comprising atarget-hybridizing sequence consisting of SEQ ID NO:24, SEQ ID NO:45,SEQ ID NO:51, or SEQ ID NO:56, including RNA equivalents and DNA/RNAchimerics thereof and further comprising a promoter sequence joined tothe 5′ end of the target hybridizing sequence; and (2) one or morereagents selected from the group consisting of (a) a capture probeoligomer comprising a target-hybridizing sequence that is configured tospecifically hybridize to an HEV target sequence, wherein the captureprobe target-hybridizing sequence is covalently attached to a sequenceor moiety that binds to an immobilized probe; (b) a detectably labeleddetection probe oligomer comprising a target-hybridizing sequence thatis from about 14 to about 28 nucleotides in length and is configured tospecifically hybridize to a target sequence contained within SEQ IDNO:39 or the complement thereof; and (c) an enzyme reagent comprising areverse transcriptase and an RNA polymerase.
 2. The kit of claim 1,wherein the at least one amplification oligomer of (a) comprises atarget-hybridizing sequence consisting of SEQ ID NO:29, SEQ ID NO:30,SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:61, SEQ ID NO:62, SEQ ID NO:64,SEQ ID NO:65, or SEQ ID NO:66, including RNA equivalents and DNA/RNAchimerics thereof.
 3. The kit of claim 1, wherein the at least oneamplification oligomer of (a) comprises a target-hybridizing sequenceconsisting of SEQ ID NO:29 or SEQ ID NO:64, including RNA equivalentsand DNA/RNA chimerics thereof.
 4. The kit of claim 1, wherein the atleast one amplification oligomer of (a) comprises the target-hybridizingsequence consisting of SEQ ID NO:28, including RNA equivalents andDNA/RNA chimerics thereof.
 5. The kit of claim 4, wherein the at leastone amplification oligomer of (a) comprises a target-hybridizingsequence consisting of SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, or SEQID NO:32, including RNA equivalents and DNA/RNA chimerics thereof. 6.The kit of claim 1, wherein the at least one amplification oligomer of(b) comprises a target-hybridizing sequence consisting of SEQ ID NO:24or SEQ ID NO:46, including RNA equivalents and DNA/RNA chimericsthereof.
 7. The kit of claim 1, wherein the at least one amplificationoligomer of (b) comprises a target-hybridizing sequence consisting ofSEQ ID NO:56, including RNA equivalents and DNA/RNA chimerics thereof.8. The kit of claim 7, wherein the nucleobase at position 1 of SEQ IDNO:56 is guanine (G).
 9. The kit of claim 1, wherein the amplificationreagent comprises an amplification oligomer as in (a)(i), anamplification oligomer as in (a)(ii), a first amplification oligomer asin (b), and a second amplification oligomer as in (b).
 10. The kit ofclaim 9, wherein the amplification oligomer as in (a)(i) comprises thetarget-hybridizing sequence consisting of SEQ ID NO: 65, or an RNAequivalent or DNA/RNA chimeric thereof; the amplification oligomer as in(a)(ii) comprises the target-hybridizing sequence consisting of SEQ IDNO: 29, or an RNA equivalent or DNA/RNA chimeric thereof; the firstamplification oligomer as in (b) comprises the target-hybridizingsequence consisting of SEQ ID NO:24, or an RNA equivalent or DNA/RNAchimeric thereof; and the second amplification oligomer as in (b)comprises the target-hybridizing sequence consisting of SEQ ID NO:56, oran RNA equivalent or DNA/RNA chimeric thereof.
 11. The kit of claim 1,wherein the amplification reagent comprises a first amplificationoligomer as in (a)(ii), a second amplification oligomer as in (a)(ii), afirst amplification oligomer as in (b), and a second amplificationoligomer as in (b).
 12. The kit of claim 1, wherein the amplificationreagent comprises a set of first, second, and third amplificationoligomers comprising a set of first, second, and thirdtarget-hybridizing sequences, respectively, wherein the set oftarget-hybridizing sequences consists of: (i) SEQ ID NO:65, SEQ IDNO:29, and SEQ ID NO:24, including RNA equivalents and DNA/RNA chimericsthereof; (ii) SEQ ID NO:65, SEQ ID NO:29, and SEQ ID NO:56, includingRNA equivalents and DNA/RNA chimerics thereof; (iii) SEQ ID NO:29, SEQID NO:24, and SEQ ID NO:56, including RNA equivalents and DNA/RNAchimerics thereof; (iv) SEQ ID NO:66, SEQ ID NO:24, and SEQ ID NO:56,including RNA equivalents and DNA/RNA chimerics thereof; (v) SEQ IDNO:65, SEQ ID NO:24, and SEQ ID NO:56, including RNA equivalents andDNA/RNA chimerics thereof; or (vi) SEQ ID NO:62, SEQ ID NO:29, and SEQID NO:56, including RNA equivalents and DNA/RNA chimerics thereof. 13.The kit of claim 1, wherein the at least one amplification oligomer of(a) comprises a target-hybridizing sequence consisting of SEQ ID NO:31,SEQ ID NO:30, SEQ ID NO:29, SEQ ID NO:66, SEQ ID NO:65, SEQ ID NO:64,SEQ ID NO:62, SEQ ID NO:35, SEQ ID NO:34, SEQ ID NO:33, or SEQ ID NO:61,including RNA equivalents and DNA/RNA chimerics thereof.
 14. The kit ofclaim 1, wherein the capture probe target-hybridizing sequence consistsof SEQ ID NO:4 or SEQ ID NO:42, including complements, DNA equivalents,and DNA/RNA chimerics thereof.
 15. The kit of claim 1, wherein thedetection probe target-hybridizing sequence consists of SEQ I NO:55 orSEQ ID NO:67, including complements, DNA equivalents, and DNA/RNAchimerics thereof.
 16. The kit of claim 1, wherein the detection probeoligomer comprises a label selected from the group consisting of (a) achemiluminescent label; (b) a fluorescent label; (c) a quencher; and (d)a combination of two or more of (a), (b), and (c).
 17. The kit of claim16, wherein the label is a chemiluminescent acridinium ester (AE)compound linked between two nucleobases of the at least one detectionprobe oligomer.
 18. The kit of claim 1, wherein the promoter sequence isa T7 promoter sequence and the RNA polymerase is a T7 RNA polymerase.19. The kit of claim 18, wherein the T7 promoter sequence has thesequence shown in SEQ ID NO:73.
 20. The kit of claim 1, wherein thereverse transcriptase is an MMLV reverse transcriptase.